In the past 2 days I have noticed as I drive along at about 50MPH my RPM will drop off a bit and then surge back up so you can actually feel the Jeep slow a bit then pick up. The fluid looks good and at the proper level. I did have some vacuum lines off and some sensors unplugged when I swapped injectors early Saturday but have no codes showing. Naturally I worry about the worst case and think transmission. I will go back and recheck all the stuff I had undone Saturday but in the mean time what transmission related stuff could I check? Thanks

 

I think your on the right track with the vacuum issue
Have you noticed any other symptoms from 1st to 4th?
and as long as your fluid looks good (not burnt) you should be fine. you could drop your pan and check the filter, maybe replace...