Audi's rock!

I have a 2000 A6 2.7t (modified) and have been having some issues with it. Slave cylinder went out, fuel pump, coolant leak, and a thermostat to name a few. I fixed some of them, but I'm stuck on this one.

I'm assuming the central locking control module went out of the car because I got the 3 open door indication on the dash and none of the windows worked. It also kept making my alarm go off (silently) which drained my battery. Totally annoyed, I removed the battery, which I found had a dead cell in it, and haven't driven the car for about 3 months. I bought an Optima for it and tried to start it. It cranks fine, but it wont turn over, I don't see the key symbol in the dash. I checked the fuel pump, it still works and I had no problems starting the car before the battery died in it. I'm lost. Could the alarm going off and draining the battery messed up something electronically? I hate taking my car anywhere because I don't trust shops too much, but I may have to suck it up and tow it somewhere. If anyone could help, I'd greatly appreciate it.