Recently I had a similar issue in my 2002 CLK430 - w208. After sitting for some time, I tried to open the top. When I pulled the lever, the windows dropped, the fronts 1/2 way, the rears all the way, then the light flashed slowly. I followed some of the other posts here to check the basics - I pulled the trunk apart and exposed the pump. The pump was full and worked for the headrests / rollbar. The relay was fine (swapped the fuel pump relay), still the same issue. checked the 3 fuses. Next step was to get the codes - unfortunately it seems that the W208 codes are accessible only through the 38-pin connector and ICarSoft MB II and I980 are incompatible with the W208. I just took the car to my local German Auto Repair shop and asked them to read, report, and clear the codes. They returned the car to me an hour later with a working top. They indicated that the soft top control module had a stored code for the cover latch. They cleared the code and manually raised and lowered the top - after that, things were fine. The mechanic asked if the battery had been removed or discharged and I let him know that the car sat idle for about 6 weeks, so the battery may have been discharged (not enough to cause issues with starting it) - he thought that the lack of amps may have caused a condition that was a defeat for the top. Charge for their service was about $150 - seems fair since swapping parts would have gotten expensive quickly. During this, I was told by an Ebay seller that the ilink400 scanner can be purchased with W208 diagnostics loaded - he claims that this tool can be used to read and reset soft top codes (and all the other control modules). At $150, I'm thinking it's worth it if it really works -- if anyone has experience with this ODBII reader, let me know.
If others have the solution to the soft top problems, post them - I found a lot of problems, but finding solutions or detailed steps to diagnose is a lot more rare.