Wow, over two years?
Do you have the original emissions label on the radiator support(sometimes on the strut support)?
It should tell you how to set the timing...... I can't remember that far back, if it was a wire harness that had to be disconnected or if you just jumper A to B in the ALDL connector......in either case, you set the timing(usually 8 degrees BTDC) with a harness disconnected, or the ALDL jumpered......loosen distributor bolt, adjust distributor to timing set on emissions label, and then tighten bolt......then reconnect harness or remove the jumper from the ALDL......now if you look at the timing, it will NOT be the same as the base timing, because now the ECM is controlling the timing....
You must have the correct ECM and PROM for your vehicle.....