Starting issues

I've got a 95 auto with the 4.0 sitting in a dorm parking lot and it won't start! I posted in mod. tech a couple days ago, but I don't think the mods I've done would affect this that much so here it goes.

At first it lost all power to everything. I got power back to everything and got it started, shut it off to put my tools away, came back and it won't start. The only code that the computer will spit out is that my battery was disconnected a little while ago.

As for the starting system, all I get is a single click from it. I put a rebuilt starter from Autozone in and the only change is that the click is a little louder. Next I replaced the starter relay, no change. I also had checked the battery and terminal connections. When I started the battery was pushing 12.76 volts. All the connections seem to be good too. If it makes a difference, I've got marine grade quick disconnects and I had just replaced the battery 3 days before this happened. It ran fine after the battery install. I've also got some exhuast mods and stereo equipment, but the amp is disconnected right now.

Sorry for the long post and thanks in advance!

Takes a lot of amps to turn over a starter, less to actuate the solenoid (the click). I´d check the battery ground at the block.
Then try and jump it with another battery (car). Just to make sure it isn´t your battery, they can fool you.
Double check the battery connections, clean (till they shine) and wipe down with a rag and solvent. Double check the ground.
I´d check the disconnects for signs of scorching and/or point welds. If you see little shiny spots (or burnt/weld places) in the poles or disconnects it´s a sign of poor contact.
I always bench test my starters with a good battery and a set of jumper cables, put the nuts on first so you don´t burn the threads.
Sounds like a poor connection, in a high amperage cable/connector someplace. Or a near dead cell in your battery.