Engine Stumbles between 1500 and 2500

Built a stroker in my 97 about a year ago. It ran fine for the first 4-5k miles. Before the stroker I had an issue where I could drive it normally, turn it off, and it would stumble after I shifted to second. The stumble would go away as soon as I let off the gas(shifting into thrid for example). I never looked into fixing it. Now the stroker does the same thing, only much worse and all the time. It doesnt matter if its cold or warm. As soon as I get through that RPM range it takes off like normal and will run fine until I have to accelerate through the range again. If I try to hold an rpm at idle it will fluctuate about 100 rpms and slowly fall. I disconnected the battery and held the key for 30 seconds, and it seemed to go away for the first 2 minutes then was back again. The o2 sensor has never been changed so I have one of those ready to go. I suspected maybe the fuel filter, but the auto part stores dont have it. Can you change only the fuel filter, or do you have to do the whole pump? Any other ideas?

I would guess throttle position sensor.

Get or use a scanner and monitor the tps% values in that area to see if they are fluctuating. You can even monitor tps with the engine off, ignition on and see if there are issues. IIRC mine is 8% without touching the pedal to 91% flooring it(get an extra 1% if I remove the floor mat).

Changed upstream o2 sensor, spark plugs, got a TPS and the sensor on the drivers side of the TB from an 01 in the junkyard. It still stumbles a little, and it smelled super rich when I was fiddling with the TB. Im guessing it just hits a rich spot and it starts throwing everything off. When I changed the sensors my CEL turned off.

The CEL comes on occasionally, and it still stumbles, although not as much. Im wondering if it isnt running too rich from incorrect sized injectors. I got the Blue top Densos from a Lincoln Mkviii 4.6.

if the cel comes on, doesnt it store the code?