SAFC2 with a S4 NA to S5 intake swap
 

So I have a 88 NA and I had my SAFC2 all set up and my car was running fine.

This weekend I installed a S5 Intake manifold and T2 secondaries and ever since than I can not get my car to run smoothly. It does not decel smoothly and lurches when i ease off the gas to shift. It also will "sputter" (i guess this is the best word to describe it) when I am in gear and holding the throttle down any less than 81%.

I know it is connected to the SAFC as when I disconnect it and jumper the yellow and white wire it works fine. Do I need to change the settings to reflect those of an S5 (06,06) instead of the S4 settings (05,05)?

Well since I got sent home early from work for missing the safety meeting I guess I can try and mess with the settings. I also think I have a vacuum leak which could be causing the problem.