No Dash Lights/Gauges, A/C, Stuck Shifter. Help!

I own a 1998 Lexus ES300 (since new) with currently just over 30K on its 3.0L V6. Obviously, I don't drive it much and it stays in the garage most of the time. I run it regularly to get things to flow and the battery to charge. However, after a long 2+ month vacation over the summer, the battery died completely. I managed to have it recharged (trickle charge) at the local auto parts store, where it checked out OK, with good voltage and no dead cells.

Unfortunately, during the removal and replacement process, the alarm went off a few times. Now, the car starts OK and the battery seems to have plenty of power but:

[*]None of the dash, radio, auto A/C, etc. Equipment and respective digital displays/gauges and lights work.
[*]Power windows and locks do not work.
[*]Remote lock/unlock/alarm does not work.
[*]Shifter will not disengage from Park unless I override it mechanically with the console mounted button.
[*]Who knows what else doesn't work. ?

I've read on the Internet that this may be due to the triggering of the alarm and the computer going into "theft mode" or maybe because of the computer losing power for too long and needing to be reset. Does anyone have any idea what may have happened and how to address this problem? Is this something I could do on my own somehow? Or, I'm I stuck with a trip to the dealer or to my local japanese auto care shop? Any information will help. Thank you! :D