Stuttery rough running

My 98 Xj has a stuttery rough run as of last night. It does not go away at the same time but rather at random. I decided to look at it after work today and it was so bad on the way home that it was bucking at 45. I think this is the fuel pump because when my other Xj's pump began to die it had a mild shaky idle for about 30 seconds. I just want to get a second opinion on a diagnosis.
Additional information is that I put a new engine in about 3k ago with a lot of new stuff. Also the fuel pump that is in the Jeep was done by a shop a few years ago since the previous owner did not work on cars (probably means the pump is s**t). The rough running will eventually go away, not necessarily when the engine warms up. Sometimes after, sometimes after a couple mins of driving. I just want to be sure that its the pump and not some sensor.

Testing the fuel pump pressure before you buy any new parts is a good idea.

So I had literally no pressure in the line when the engine was off because this pump does not hold fuel in the line when the engine is not running. I decided to just go through with changing the new pump because the old one was garbage anyways. I put the new pump in and tested the new pump and this thing still runs shaky. This pump woks properly so I inspected the fuel lines as well as checked for pressure and both are good... Someone I know mentioned it could be running rich but im not getting any codes.

If not the fuel pump, then O2 sensors and/or a cracked exhaust manifold.

Im not getting codes from the O2 sensors but still not out of the question. Ill start by checking the exhaust. The engine has only been in for a little over 2k so the bolts could have moved despite being torqued appropriately

Not getting O2 codes does not mean they are operating correctly.

TEST the O2 sensors.

My 88 MJ died on me a few weeks ago. Replaced the fuel pump and one of the lines had fallen off the old pump. Now it's running like yours, stuttery and rough. I'm going to try the fuel filter tomorrow. I assume something in the lines caused this.