This post maybe a little long but all important details to address.If not interested I have a TLDR summary.
I have an almost sadamstic relationship with Mercedes. I'm terrified of leaving my car with the dealer. The last four times I left my car/cars with the dealership it came back with problems. My first AMG was a CLA45 when it first launched. Took my car in for its first service at 10k miles without a single hiccup. Decided to reward myself for driving sensibly and properly breaking in the engine by taking it to angels crest. LITERALLY two days after getting the car back, I have pieces of my turbo coming out of my exhaust. Long story short, lemoned the CLA45 but was faced with another tough decision. C63 w204 or c63s...obviously I picked the fun one. Off I go with my new c63 507 and all the warranties and services they had to offer without an LSD but that's another story for another time.(**** Mercedes of Encino)
A little under a year later my first service comes around I take it back to Rusnak of Arcadia deciding that the CLA45 was more of an engineering fault than the dealership. I get my car back after a ****ing oil change and 7 point diagnoses and my car starts making knocking noises. I take it back around august of last year and get it back october. On Halloween my car breaks down on the highway stalls and dies. I have to restart the car it'll drive for an it and then die. Off it goes to rusnak and from ****ing November 1st until god damn March. My service advisor told me every week "If everything goes right your car will be ready by next week" from Christmas until I got it back in march.
During this time I've been buying all the mods for the car so Row airboxes, kw-v3, kleemann lth, eurocharged tune AP cat back. Needless to say I are broke. Apparently so is my car. The Indy that did the installations asked "Did you try to install these yourself? All the bolts are loose or missing from your engine" I just told them to bolt everything down I want going back to the dealership. Now I'm dealing with a persistent lean LTFT condition and I'm finding sensors that don't belong in my car installed and plugged in to somewhere...and missing 60hp with my B2 service coming up. I have a very tangible phobia of dealerships now and don't know where to go.
In April I get a surprise call from Mercedes and they were offering me 4 grand and carbon listener plates for all of my troubles. I got the 4 grand they forgot the listened plates(ha is sue)I got my car dynoed twice first time everyone told me I looked rich and the second time everyone told me I looked lean. I dynoed stock, tune 6 and tune 7 from EC all three results were identical. 415hp to the wheels.I've taken my car to Serge from benzworks and told me he cleared my stored codes and I should be fine. I asked him to examine my car which he did for maybe 30 minutes. Told me I had a stored code for maf sensor and reset my adaption. Nothing changed. Hunted for vaccum leak with carb, smoke and gaskets nothing's changed. My LTFT are indefinitely postive and lower during acceleration. I have new mafs and am running out of options and money. I'm a kid in college putting all my money into this car with no results. I can take it to the dealership but I feel they will only make it worse. My B2 is coming up so I have to but I'm afraid with all my mods they will try something shady.

TLDR: I have the worst experience with Mercedes dealerships it's almost unreal. Spent all the moneys on mods to find I am missing 60hp. Spend all the money on finding solution coming up with no resolution only more problems. My B2 service is coming need advice in case the steaershio tries to be shady and am seeking a dependable dealership in SoCal.

Searching for the common denominator here...

First thing I would do is return the car to stock and send it to MB. Your post was kind of a long run on so forgive me, but aren't you in a 507 with a warranty? If so, return it to stock and send it back.

I've had nothing but positive experiences at my dealer. Just keeping shopping around for a MB dealer and eventually you'll find one that knocks it out of the park day after day.

Sorry to hear of all your troubles. Are you on AMG SoCal Lounge group on Facebook? For warranty work, a few of us have had great experiences with MB Laguna Niguel, myself included. Recommend S.A. Tarek Saba, and AMG Tech Anthony Pickering - very skilled and professional.

Anything additional to warranty work, we in SoCal are blessed with 3 incredibly talented AMG Master Techs: Matt Stockwell of Leistung Autohaus, Chris Mattox of Star Motorwërks, and as you already mentioned, Serge of Benzworks. Michael Long (also in the FB group above) is also highly regarded. If MB NG can't resolve issue, or you need second opinions, these individuals are exceptional.
Best of luck!

Where are you exactly?

Star Motor Werks in Costa Mesa. Hands down the go to place for all things AMG service in SoCal. Also kid in college putting all his money into a car sounds like a really bad idea. I'd listen because I just finished college this May without debt and money in my pocket. I wouldn't blow it all on car mods because we all know that's a slippery slope. If you got 4 grand in your bank account use it to take the car back to stock, and leave it that way until the car is running the way it's supposed to. If you have a warranty don't give Mercedes a good reason to deny a claim. That's just pissing money away. I'd just expect to spend a lot of money putting the car back to the way Mercedes designed it to come off the assembly line, and leave it that way for a long enough time to at least enjoy the car first.

ok...learn to break up your sentences into paragraphs.

Many of us have experienced "knocking". its generally diagnosed as lifter noise. I've experienced it while using Mobil 1, which is factory fill. I haven't once dealt with it when running Motul.

As far as your car no start issue...good luck. That must have been a headache.

In regards to missing bolts, etc...well my car had a valve cover glued back together by Mercedes of Beverly Hills. Can I prove it? No I cannot because it failed 10k later. I solely have my 2007 E63 worked on by Indy's that I know personally or have a good relationship with to avoid such issues.

I'd focus more on learning grammar and spelling, maybe sentence structure, and less on pouring all of your money into a car as a college kid. What college do you go to, because it's not working.

You have a warranty, why not find another dealer you can bring the car to? Why did you mod it up in the first place if there was so much wrong with it? Why did you not lemon this car as well? Lot of bad decisions along the way there, sorry. The second your car was at the dealer with no explanation or resolution of your problems for months, you should have raised holy hell with MB corporate and gotten the **** out of that thing. It's just a car, and apparently a terminally broken one. Then you mod it up, right.

Sounds like it's going to be an expensive lesson for you.

Im not sure if you ever tried using mbworld on an iPhone when it gets past a certain point you can't see what you are typing. It kinda makes proof reading and structing difficult on a mobile device. I'll edit it when I'm on a desktop. How many times do you press "space" to equal a "tab"? Regardless, to address your other points.

My c63 at the time it broke down on the highway was well past the one year mark to be deemed a lemon in California. My car felt fine after I got it back from the long hiatus, after they had "fixed" my car. I decided to finally mod my car, because while discussing my compensation I inquired about modifications.corporate assured me, that unless the mod proved to be the culprit they can't hold it against me.

The dealership I bought my car, Mercedes of Encino, tried telling me my C63 came with a LSD proceeded to hide the buildsheet in the little stupid gift bag he only handed over after I had made the purchase. When I discovered I did not have one he laughed it off saying "ohh lsd I thought you meant ESP every Mercedes has one. I immediately asked for my money back and I was going to another dealership he shot me the old "value of the car drops the moment you drive it off the lot". There are a few other dealerships I visited with equally bad experiences.

Ok, fair enough.

You should just drive it into a wall then, take off the mods, and put them on the replacement car.

Seriously though, find a new dealer. You have a warranty, don't drop another dime on the thing until it's fixed. I'd even consider turning it back to stock completely.

This post maybe a little long but all important details to address. If not interested I have a TLDR summary.

I have an almost sadamstic relationship with Mercedes. I'm terrified of leaving my car with the dealer. The last four times I left my car/cars with the dealership it came back with problems.

My first AMG was a CLA45 when it first launched. Took my car in for its first service at 10k miles without a single hiccup. Decided to reward myself for driving sensibly and properly breaking in the engine by taking it to angels crest. LITERALLY two days after getting the car back, I have pieces of my turbo coming out of my exhaust.

Long story short, lemoned the CLA45 but was faced with another tough decision. C63 w204 or c63s...obviously I picked the fun one. Off I go with my new c63 507 and all the warranties and services they had to offer without an LSD but that's another story for another time.(**** Mercedes of Encino)

A little under a year later my first service comes around I take it back to Rusnak of Arcadia deciding that the CLA45 was more of an engineering fault than the dealership. I get my car back after a ****ing oil change and 7 point diagnoses and my car starts making knocking noises. I take it back around august of last year and get it back october.

On Halloween my car breaks down on the highway stalls and dies. I have to restart the car it'll drive for an it and then die. Off it goes to rusnak and from ****ing November 1st until god damn March. My service advisor told me every week "If everything goes right your car will be ready by next week" from Christmas until I got it back in march.

During this time I've been buying all the mods for the car so Row airboxes, kw-v3, kleemann lth, eurocharged tune AP cat back. Needless to say I are broke. Apparently so is my car. The Indy that did the installations asked "Did you try to install these yourself? All the bolts are loose or missing from your engine" I just told them to bolt everything down I want going back to the dealership.

Now I'm dealing with a persistent lean LTFT condition and I'm finding sensors that don't belong in my car installed and plugged in to somewhere...and missing 60hp with my B2 service coming up. I have a very tangible phobia of dealerships now and don't know where to go.

In April I get a surprise call from Mercedes and they were offering me 4 grand and carbon listener plates for all of my troubles. I got the 4 grand they forgot the listened plates(ha is sue)I got my car dynoed twice first time everyone told me I looked rich and the second time everyone told me I looked lean. I dynoed stock, tune 6 and tune 7 from EC all three results were identical. 415hp to the wheels.

I've taken my car to Serge from benzworks and told me he cleared my stored codes and I should be fine. I asked him to examine my car which he did for maybe 30 minutes. Told me I had a stored code for maf sensor and reset my adaption. Nothing changed. Hunted for vaccum leak with carb, smoke and gaskets nothing's changed. My LTFT are indefinitely postive and lower during acceleration. I have new mafs and am running out of options and money. I'm a kid in college putting all my money into this car with no results. I can take it to the dealership but I feel they will only make it worse. My B2 is coming up so I have to but I'm afraid with all my mods they will try something shady.

TLDR: I have the worst experience with Mercedes dealerships it's almost unreal. Spent all the moneys on mods to find I am missing 60hp. Spend all the money on finding solution coming up with no resolution only more problems. My B2 service is coming need advice in case the steaershio tries to be shady and am seeking a dependable dealership in SoCal.

Added spacing. Hope this makes it better for everyone. Feel free
To edit your OP with this.

You have warranty, so you shouldn't be trying to fix it.
Return the car to stock, and take it to a dealer that knows what they are doing.
Once it's fixed properly, put your mods back and enjoy.