Weird ignition problem....

[Kalus]

MSII v3.0 board, v2.35 firmware on 2002 Jeep 4.0l I6.
I have used an electronic distributor from an earlier model (1999) and made a new vaned wheel for it. On idle it misses on 1 or 2 cyls. Checking the timing with the timing light I found it to be retarded (firing at TDC or thereabouts), so using the trigger wizard I set the offset to show the correct advance (10 Deg BTDC, -9.0 offset) as displayed. Went to take it for a run and it still misses at idle and detonates like mad when even using the smallest amount of throttle. I set the offset back to +20, and the miss goes away, but there is very little power.
Any ideas what this could be???

[MegaScott]

Are the Vanes on your dizzy concentric? are there some windows or slots wider than others?

You may be triggering off the wrong edge of the input wave form, that can cause a cylinder or two to be retarded or advanced significantly more than the others.