Odd Overdrive shift issues

[schiavonske1013]

Hi guys, I have sort of an odd problem and was thinking maybe you could help. I have a 96 5.0 Explorer. Never had any major issues with it until now. A few months ago it started shaking when it would try to shift out of overdrive. For example if I was coasting at 45 and it was in OD and I pushed the gas lightly, it would shake violently and then shift out of OD. It ended up throwing a misfire code and found that both coil packs were junk, so all plugs wires and coil packs were changed. Everything has run fine except it still hesitates for a few seconds while shifting out of OD, no shaking though. My father is a mechanic, I'm ASE certified but don't fix cars at all except for my own now, but haven't had a whole lot of time to tear into this. We checked the drive shafts, transfer case, rear end and a few sensors but nothing seemed wrong. Even his transmission guy said it shifted great and the torque converter wasn't causing an issue. One thing he noticed is that I have 3 of 4 cats chopped out and straight piped. Since it's so old MA doesn't require emissions so I had them removed when they wen't bad. He said the lack of pressure may be causing some touchy shifting with the computer. I was wondering if there is any chance you would know if this can be true? I know this is a bit long and I appreciate any insight you might have.