Cal,Jeff,
Give me a call this afternoon, if you are still having problems. I thought you were fixed and up and running. Also, re-verify your crank reference angle. 12 degrees with a BHJ is possible but unusual.
I checked it again and the reference angle is 14. What I have been doing is setting the timing map at 25 then I measure off 1.45" on the balancer and make a mark to represent 25 degrees BTDC. I bring up the rpm to about 2000 rpm and shoot number 1 with a timing light. Then adjust the reference angle to get my 25 degree balancer mark to line up with 0 mark on the plastic marker on the block. If this procedure is correct, maybe the ring on the balancer changing positions.
Also I made a mistake identifying the metal tab on the distributor. I used the suggestion that Otto gave me and changed the tps setting to 30% and found number 3 responded to the change in the individual cylinder correction table on the balancer. Using the firing order of 165432; to get the engine to read #3, I think I would have to enter 4 in firing order sync. box.
With all this done the car idles O.K. but it drives terrible. Since I also changed to 160# injectors and a new program, maybe it needs to be adjusted but it seems to be way off. What number are you guys using in the XFI for injector opening time (ms) for 160# injectors. Mine has .9 and I think it should be higher.
Jeff