I have a 95 2door and just got a 97 4door that has a dead motor.  I got the 4 door because I need a front knuckle.  Should I change all of the suspension?  Will the 4 door stuff give me any lift, or better brakes? 

What do you guys think of changing the complete wiring harness and computer to upgrade to the OBDII stuff?  I know that would be a lot of work, but would it be worth it?

4 door brakes will be a good improvement on a 2 door.  Suspension wont give you much lift but, if you want to do it, go ahead if you have the springs and what-not already   

Cant help you with the OBDII question.  Im stuck with OBDI , havent had the pleasure of using the other..