The 2 cars were a 98 Rs/MT (my totally fine running vehicle) and I bought a 97 Gs/AT to swap into. After doing the swap I have this problem.. ^^^

Did you swap the wire harnesses as well? The ecu pin outs are different between 97 and 98.

http://www.2gnt.com/index.php?d=ECU_Pinout

Okay that must be my problem thanks dude!! Is there a recommended fix besides swapping the whole harness

Also went to reading th pin outs seeing that brown wire activates cylinder 2&4 and black and blue activates 1&3 would this be right considering the 1&4 cylinder and the 2&3 cylinders each work off separate halfs of the coil?? Maybe a miss print?

So if I got a 1997 m/t ecu it would fix problem? or could I re wire something?

I had an idea can I just put the original automati ecu back in to see if that fixes it?

I think it's a miss print or the person labeled them as the firing order rather than cyl #. You can try the auto ecu to check that off the list, but I believe the auto ecu will throw a check engine light because the trans computer won't be there. Also the auto ecu rpm limit is around 500 rpms lower.

You could:
-Swap the harnesses
-Get a 98 manual ecu
-Or try moving the ignition pins to the correct 98 pin out.

Hey man thanks for all your advice and input means a lot!!! Got her running fairly well now using the auto ecu (fix it) I think after I finish up a few things I'll either try to move the pins in the plug or wither order the AFX 1997 computer, isn't this computer tuneable? I wanna build another 420a engine and turbo. Would this computer be ideal?

The AFX computer is from Howell

Don't waste any money on the afx ecu. The 420a ecu is not able to be tuned without expensive Chrysler hardware.

Your best bet is megasquirt for tuning.