Ok well to start off switching batteries while the car is running is plain stupid the things your going to have checked and maybe replaced is as follows : the starter motor the ecu the coil pack for v6 distributor and cool v8 and the alternator
Unfortunately heathsydm is right, that was a stupid thing to do, you could do it in the old days before the cars had computers but now you cant, Alternators are irregular in the amount of Volts and Amps they put out and the battery even if it is dead flat will act to regulate this voltage and amperage, once you take the battery out while it is running the alternator will surge in voltage and amperage to compensate for the lack of a battery often killing the computer.
However all is not lost, try checking all the fusible links first, there is a little black cover with 5 main fuses in it, down low between the battery and the the main relay panel, take of the little long black cover and check all five main fuses, then check all your fuses under the dash especially the ecu fuses, if all of these are ok then check the ecu relay under the big black cover between the shock tower and the battery, switch out the ecu relay and with another and test the engine, if still no joy I would imagine you have fried the ECU, I would borrow one from one of your friends first and put it in to see if it will run, if so take your old ecu to the wreckers so they can match the numbers and get yourself another one. Hope this helps - Jon.