john deer green

I just got a new motor put in my 93 xj and it has been running fine for the first 200 miles. Yesterday after I drove it to work and let it sit all day I started it and let it warm up it idled fine then got in it and started driving. For the first 5 miles or so I was dlin about 45 and aboue 2200 rpms and it started to buck like it was stalling or not wanting to shift down if I would push the gas to the floor it would perk back up but still struggled to get past 2,000 rpms. But after about 5 miles it cleared up and ran fine for the rest of the 90 mile journey home. Then this morni g it did the same thing . The engine is at running temp at the time of the studdering I was woundering if maybe it could be the transmission not wanting to kick down and stalling it out ? Does anyone have any ideas any help would be appriciated thanks.