Hi,
Congrats on completing your lift
It would have been best if you had disconnected the battery before taking the Jeep apart, as leaving it sit over time with stuff still connected can run down the battery due to what i'd call "phantom" loads (i.e. the clock, vehicle computer, etc..) which actually use some power even when the Jeep is off.
However, the "phantom" loads should NOT drain the battery. It is normal for them to run it down slightly though.
The most important question here is what was the voltage that the battery was run down to? If it was under 7-8 volts, it's almost certain the battery is ruined. The reason for this is that standard car batteries are NOT designed for (and cannot withstand) being drained past 60+ or so % charged. Deep cycles are more tolerant of being drained down, but can still be damaged if done frequently or drained to far down.
What happens is that you risk damaging or reversing a battery cell (of which there are 6 on a 12 volt battery). Even if you were able to charge the battery back up to 12+ volts after it had been drained, a cell could still be bad, thus deratting the current output of the battery. The starter motor requires alot of current so if your battery cannot supply it, you don't start the Jeep. Try putting a smaller load on the battery (like some tail light bulbs) and see if the voltage rapidly drops or not.
Also check that it is charging properly. Most 12 volt batteries are 100% charged at around 13.4 volts
-Nick
