crank position sensor orientation question

A buddy of mine just stroked an 89 XJ renix motor and stuffed it into his CJ-5. It idles fine, perhaps a little rich for the first few minutes with a dumb computer, but settles down. vaccum is good, advance is good, timing is @12 TDC. Problem is when it is advanced above idle. Just won't run for dog $hit. I spent a solid 9 hours over 2 days going through this engine. Redid the lower end, upper end, metered all the ECU connections, tested all the sensors. Even replaced the ones we couldn't prove. ie TPS and O2.
Question is: When he modified the bell housing to fit the CKPS, it ended up installed approx 1/8th - 1/4 inch lower on the bell housing than stock. Would the fact that the ckps is lower on the bell housing and hence seeing the pickup notches sooner than normal contribute to the appearent (sp) miss fire above idle? It seems intuative that the smaller circle would result in a faster signal input to the ECU, hence a quicker firing of the injectors when we have an open valve based on camshaft position. Just looking for a check on my thinking.
D.

Never Mind: As an edit. He located the CKPS 1/4 inch over on the radius of the bell housing, not vertically down the bell housing. As I understand the pickups to operate, the orientation of the sensor around the circumference of the bell housing will not matter, as the crankshaft position is determined by the one larger pickup size over the others, creating a longe pulse wave.

when you say "lower' wich way do you mean.Lower into the towards the fly wheel or lower in position as in rotation and which way did it end up after stock position clockwise as viewed from the back side or counter clock wise?

See the edit. I just spoke with him, the relocation was 1/4 inch around the circumference. ie at 12:30 vice 12:00.
As a side note he didn't use the 89 bell housing because of the T-18 tranny in the CJ5.

D.

it seems like the crank timing is off. the sensor sould be pretty much be in the same location as it was on the xj trans.it can be moved slightly to advance the timming or retard it.mine has been modified to advance it.plus it may have a weak signal as it may not have the correct flywheel to sensor air gap.as a resort you can see a sensor on a simular year xj --87 -90 renix set up and mark on the eng block and see where it actually ended up on the cj housing.

just read the edit. it needs to be in the stock location because it uses the crank sensor to detirmine EXACTLY where the # 1 and # 6 cylinder and fires the injectors and the timing think of it as distribur if it not located where it needs to be it wont "fire " correctly