Tony:
I have a 100% factory tune in my car. I have never hooked up anything to the factory ecu.
After I installed the Baumann kit it now shifts @ 5200 every run.
Plus, I can still manually shift it if I want. ( at any rpm)
I just need a ratchet shifter to make it safer to hit the gears.
In a some what related note (or maybe it's not)..this is what I found out about the 94-95 Mustangs.
You might want to check your throttle body opening with the gas pedal all the way to the floor.
My TB would not open up 100% until I removed the carpet and sound deadener under the pedal.
Before, it was like 90 % opened and my car was inconsistent.
I removed the carpet under it and now it's 100% opened every time I stab the pedal.
Whether or not having inconsistent throttle blade openings affected the shift points I do not know, but I feel confident having the blade opened 100% every run has helped the computer in regards to the electronic shift points.