Is that the original ECU cal ID too? Symptoms all point to a mismatched ROM type. The D00 files aren't backward compatible and vice versa.

How do you mean it won't come out of programming mode? Does it not state flash complete? Do you clear all DTCs in the final writing stage?

It is the original as far as I know. It says flash complete and 1 dtc read, I clear it and after that it shows 5 dtc' cleared and shows as follows:
UO122
UO131
UO100
UO122
UO131
And says they cleared. But if I run a dtc check only UO100 cleared. As far as not coming out of programming mode...from what I've read that when you flash the ECU, it turns off all other ECM's and such, which it has done, problem is it doesn't turn them back on after I'm done! May just need to be something Perrin and I work with Ecutek to figure out.

Check battery volts
check fuses
check any plugs socket wiring you touched or moved

remove battery cable then press brake pedal leave for five minutes then reconnect, check both battery terminals and earth connections.

sounds like somthing on CAN bus is not happy it might be just one module effecting communication on the buss

if you have techstream run can buss diagnostics

pretty sure techsstream will work with ecutek cables

Checked all that good stuff and no progress. I've got Ecutek connecting remotely in the morning, I'll up date everyone on what was found.

Be interested to see what they find , it does look like a corrupt or incomparable rom has been flashed somehow.

Looks like I missed a fuse! The 140a fusible like was blown on the battery terminal. Pulled a noob move and didn't disconnect the negative before FI install and when it disconnected the alternator I shorted the circuit! *head hung low in shame* $13.50 and two days and I'll be up and running!

Thank you for the advice everyone!

I want to thank Chris Cone at Perrin Performance and Mervyn at Ecutek for all the effort they put in to helping me!