I have two of these systems.
I would suggest starting over with a tune. Sounds like you have some IAC stuff moved around.
Did you add to the fuel map with you switched to E85?
I started with the tunes included and had to do very little with them. I added timing at idle on both and made some small crank fuel changes for better starting. The closed loop built the rest of the fuel map.
Switching to E85 is not just a swap a new map needs to be built.
454 ci FTI LS3's, Mast 4500, 4 hole TB, c4 8" converter. FTI hyd roller, Holley EFI
Street car pump gas.
9.24 143.58 1.33 3.73 5.84 116.21
13 Hot Rod Drag Week SS-BB-NA Winner