Engine running rough @ 3,500 rpm

I recently swapped the engine to another 4.0 after a blown rod. It runs fine under 3,500 rpm, then when it reaches that range it will have sporadic backfires and run very roughly and will no longer climb Rpms. Also when it shifts into third gear going around 45 mph if you give it a small amount of gas it starts to go up then returns to rpm at 45 mph, but if you give it lots of gas it will go faster, so its like there is an inoperable range.
The engine is not reading any codes.
I've already swapped its tps and cps. New fuel pump with good fuel pressure.
Any suggestions?

O2 sensor can give intermittent non stored codes. The O2 sensor going out usually starts out subtle and gets worse, it may not trip a stored code. My rear O2 sensor was broken completely off and never tripped a code.

I usually look for fuel starvation or sporadic spark to ground issues. The higher the RPM the better (crisper) your spark has to be.

yeah, I replaced the O2 sensor along with fuel injectors, I forgot to mention that.

Anyone with ideas? im getting to the end of my rope with it.

dunno. as a side note, i know this guy also has new plugs, wires, coolant sensor, fuel filter, cap ... in addition to the new pump, oxygen sensor and fuel regulator mentioned above... Also, I'm sure its obvious enough maybe from the username, but this is his 1994 cherokee, so theres no after cat O2 sensor, so the new Oxygen sensor up front shouldn't be effected. Also, it has a new exhuast header installed so theres no exhaust leak - which would cause a rich condition rather then fuel starvation. Seems that its not sporadic misfire, but maybe #3 or #4 consistently when you get up around 3300 rpm.

I'm kinda clueless at this point, just because everything is so new, and the engine has very few miles on it. Obviously the truck has had alot of money thrown into it without anything fixing the issue, so most of the obvious things imho have been eliminated as options.

I'm not sure that the problem could be caused by this... but maybe the coil doesn't like that rpm/has an intermittent problem? Or maybe like 8mud was saying about leaning out - map sensor has issues? I'm not real familiar with how either of those going bad could effect the ignition system, especially just at 3500 rpm, but maybe someone else could confirm those theories...

i helped this guy out yesterday... tried replacing ignition coil and map sensor... still nothing. nothing really left to throw money at, and everything appears to be fine - but it consistently backfires at 3500rpm but runs about perfect under that.

cps..

distributor..

My MJ had a terrific miss at 2000 R"PM, once past that, it ran fine. Turned out to be the manifold air temp sensor. took it out and cleaned it, then burnt it off a little with a torch. At about the same time, I installed a HEAVY ground wire from the block to the firewall, so I really don't know which of these two things fixed it....but, voila, no more misses....if any sensor has a resistance reading that is a little out of spec and your ground is iffy it will drive you crazy trying to find it.

I would check the windows on the flex plate the CPS uses for reference, it might have damage,I have seen them get damaged when installing an engine... what scanner are you using? Can you read data stream as it is running? I have also seen flex plates warped just enough side to side they do not run true and cause what you are talking about........You need to get yourself a remote starter button so you can spin the motor around and look at every inch of the flex plate, I have removed the inspection plate and the cps to get a look at the interrupter windows while cranking with the remote starter......takes some time,....remember you can not have any damaged windows what so ever or it will never run right...... Was the Jeep running normal untill the engine let go?:explosion

hmm, thats where we'll look next. the jeep has just kinda been sitting for a while, but yes, it ran fine before the motor swap. the flexplate being damaged is certainly a possibility.

Let me know if you find anything.....also if you are tired of the Jeep would you consider selling it?