Engine Weird Idle/cruising Misfire

Alright guys coming back to my roots here at Stanget hoping to solve this one. Recently swapped a PI 2v 4.6 with a Stroker kit into my 96 gt. Along the way I deleted my EGR because with Longtubes it's darn near impossible to put all that crap back on. Problem is I've had a little bit of a miss at idle ever since I put this motor in. The miss I can deal with but here's the real issue. The car surges and bucks under quarter to half throttle. I can't seem to get it to happen until 4 and it's bad in 5th. Weirdest part is it's pretty darn bad from 1100 to about 2200 and then it cleans up. Also if I continue to push it when it's bucking it backfires in what sounds like the headers (might not be in headers though). I've pulled the codes and there's a couple EGR codes in there and then it's showed a miss in cylinder 3 a couple times and more recently a miss in cylinder 5.

What I've tried:
Fuel filter change. Checked and regapped all of spark plugs (they're a year old). Unplugged MAF while running, car died. Replaced both cool packs *sigh*. Swapped plug wires to missing cylinder to verify they aren't the issue. Checked fuel pressure, took a little but came out to like 31 running. Checked the vacuum lines and they all seem fine. Swapped out injector on missing cylinder with a spare to verify injector isn't culprit. Also compression tested cylinder 3 and it read just fine. And lastly I have an SCT X4 on the way to shut off the EGR to hopefully fix this madness...

Also important to note with my current set up I'm getting 4 less miles to the gallon and I haven't been romping much so mileage is rough. And when I used our little code reader here at home it claims the STFT is 20% on both banks and the LTFT is 7% on both banks which from what I've read is absurdly high. I haven't tuned the car but I'm afraid to dyno tune it with current issues because I don't think a tune will solve it.

All in all I don't know what the issue is. Thought I had it partially nailed down because of cylinder 3 but now I got cylinder 5 to miss so I don't think it's a bad plug,injector, or the wiring. Could the EGR cause all this trouble? I want to naively say yes and that the tuner will fix it but it just doesn't add up. Any help is greatly appreciated.

Thanks

It is the full PI motor.

Well at first I pulled the egr system off the throttle body, used a block off plate, capped the header Bunge and removed the DPFE sensor left the vacuum lines open. However now I reconnected the vacuum lines put the egr system back on and used the penny method where the tube meets the egr valve to block it and it runs the same (still no DPFE sensor).

The evap system didn't seem to care if the 3 lines were plugged into the egr system or not (should do further testing with that).

Factory looms and wires are used. They're numbered so they're not messed up. Coil packs are new so they shouldn't be the issue. I've tried that trick but didn't see anything. It's possible that it's vacuum line related but I haven't changed any of the lines since my old engine and it didn't have any vacuum issues.

Also don't think it's wires because I changed wire 3 with wire 7 and it ran no different. Oh and important to mention I can rev her from idle to redline in neutral and it goes smooth. Only under load do I get that shudder and backfire I mentioned.

wmburns said:

What if the problem in the #5? Since 3/5 are are part of a waste spark system, the problem "could" be in either pair.

The program in the stock PCM is going to be for a non-PI motor. But you have a full PI motor. The timing curve is very different between non-PI and PI. One of the power causes for "bucking" is timing related. So if sure the ignition is perfect then maybe a tune would solve the issue.

Click to expand...

See that would make a whole lot of sense because I almost wondered if the timing was off (bought the motor used and never checked the timing, stock cams/heads so I assumed it was good). I wasn't aware that the timing was different between the two nor the whole spark waste system... Would I be able to test any of that with tuner I'm getting? I know it data logs but I don't know how far in depth it gets as far as all the data collection.