Could it be a short?

A conundrum for those more mechanically inclined than I am...I have an '03 6 4 cyl. w/67k miles (only owner).  I went to pull into traffic and all the getup disappeared, so I immediately pulled into a parking lot and noticed the battery light was on and the car was stuck in 3rd gear.  I was late for work, so I stole my wife's car and when I came home that night the battery was completely dead.  I got a new one, but no help.  It starts up fine and goes straight into 3rd gear when put in drive and the battery light is on.  I'm guessing that a diagnostic will tell me the alternator is dead, but I'm worried there are computer issues.  Could the alternator issue be causing this? Is it a short?  Or am I screwed on a computer issue?  By the way, anyone know how to reset the computer?

Thanks in advance!