Hey guys need some help on this ....

Okay so the 95 type eprom ecu came in the mail today so i went an hooked it up to my 99 gst hoping its in perfect working condition. pluged all the wires in the ecu, fired it up an it doesnt start... go on tuners an it says to switch spark plug wires #1 with #2 and #3 with #4 so i do an the car starts, but the car will bearly stay running.....Im waiting to send to dsmlink an i did select the the cas inversion option... A couple questions is should my car still run really bad even with the plug wires switched or is there actually something wrong with the ecu?????? will i still need to keep the wires like this even when i recieve dsmlink??? will the cas solve this problem an should i just go ahead an send it out?????
Please help wisemen.....
THANKS!!
Regards Paul