You are throwing 2, 3, 8, 11 and 12 on the left bank. That doesn't make sense as the TPS and battery voltage are one in the same (ie, not two batteries or two TPSs).
Are you sure codes are clearing? when you do the jumper, insert it, turn the key to on position without starting, and you should hear a click. Then remove jumper and turn key on 4 times and see if codes are clear.
if they are clear, and those codes are still on one side, I would
1) switch LIE's and see if the codes move from one bank to the other
2) check the two ground straps on the engine to frame (assuming you cleaned these up when you reinstalled engine).
on setting the idle: page 42 and 43, summarized as follows:
1) warm up engine until fans come on
2) close the two air bypass screws and make sure idle speed doesn't fall below 800-900 rpm. if you need to raise it, there is a screw encased in a holder that controls the butterfly positions, use that to balance the banks and keep idle around 900rpm.
3) now use the air bypass screws to raise idle to 1130 - 1180.
4) verify timing
5) set TPS (1.5 degrees or 0.5v)
6) Crack throttles open a little and ensure banks flow evenly
If you need the pages, let me know will scan.
