So, just what is the voltage reading now with the "new" alternator installed. 14.1 or 14.2 with engine running
For trying to be frugal, you sure have poor deductive diagnostic reasoning.
Did you load test the batteries, or how about an alternator output check, just because the brushes are a certain length does not mean the unit is right. Possible shorting of the alternator when your seller removed it or if the car was involved in a crash then possible to short out the charging system at that time. Used is not always the best value when buying electrical items. They all look good, but the operation can be sketchy, as you have found.
To repeat myself, have never in my life seen any 12V battery in normal usage give 13V readings.

Well than critter I guess my Deka battery is one of a kind. As for your opinion about my deductive diagnostic reasoning its called COMPROMISING and TRYING!!! Ok now back to the subject when I am about to turn the car on it says 12.5V when car is cranked and engine is running it stays at 14.0V when I turn the headlights on it says 13.8V. I think it's the aux battery. Your right about the used alternators but I think this one works. Because it obviously charges and I can drive for hrs just that the convention function message keeps going on and off idk

Disconnect the aux battery negative connection, test voltage on the aux batt. Do not drive the car as the aux battery is there to power the brakes, but with the aux bat disconnected start the car and read the voltage, this way you are only powering the rear trunk batt. The alternator should have enough power capability to maintain 14.1V or 14.2V with the car running and the lights, radio and the AC at idle. If the aux batt is showing less than 12.5 after sitting for a while then it is time for replacement, 5 years out of a battery is good, trouble usually starts after this time frame. The power(amperage) comes from the alternator and the voltage is stabilized by the regulator, without the reg then the voltage would rise and fall according to engine RPM and at high RPMs the voltage would rise to 16-18volts which will harm the electrics of the car. Compromising and trying is expensive and wasteful of time. When in normal operation the power is distributed to recharge both batteries, if the front bat is low then possibly your trunk battery is being allowed to drain below a threshold which gives you the dash comments, because the aux bat is taking too much charge for too long.

You know I read ^ this reply of yours several times. Today my idler pulley the plastic part I was checking the spinning ratio of the belts and I Fu**in got my finger caught in the plastic of the idler pulley. The EDGE of the plastic pulley came off and my finger is now twice the size and my finger has 6 rib lines from each thread of the pulley on my finger. Even though the edge came off the pulley it should still be functional. Because I put the belt back on and it works the belt spins. all 6 ribs of the pulley are still there of course I didn't drive it. I guess my car attacked me back for kicking its fender. I'm going to give it a few days my finger is really bad I put alcohol on it and bandaged it. I am lucky the pulley was plastic if it was metal forget it. I could had lost a finger. I appreciate your reply I am going to just buy dat aux battery hope it does the trick for me. When I first pit that alternator in and when battery's were fully charged 14.2V now it's reading 13.8-13.9V maybe the aux is causing that. Also you are right when my alternator blew I kept forcing the car to turn on. I would use jumper cables from my neighbor and keep turning the car on drive around my block with the messages and cone back. Man this DEKA battery is one heck of a strong battery.

Wow Russ, that is quite the adventure, that finger will be really painful for a while because when you put it through the pulley it twisted your finger, you might want to check to see if you broke it. Before you go out and purchase an aux battery measure the voltage of it with the car off, I believe you will see below 12.2V, with the key on depress the brake pedal and watch the voltage on the aux, it will probably dump below whatever the first voltage was.
Again sorry about the finger, fingers have many nerves in them and the pain is indescribable, try holding it up should reduce the pounding.

Thanks yea thus finger is a pain in the a**. However it dident completely twist my finger.it is still swollen but I'm going to give it two more days. If my finger swells and remains the same ima gonna go get it checked out. Also used the voltage tester aux battery is reading 11.6V rear battery 12.8V this is with the car turned off

Good to find that low voltage on the aux batt, now with the car running are you seeing a rise in voltage in the aux, this will show you that the charge is being sent to the AUX through the module that feeds both batteries in your car. This is just a check. But it still looks like the AUX is toast. Hope the finger is getting better.