What's the difference between having an auto or 5 speed, is one better than the other?
Your 88 2.5 should be paired to a Aisin-Warner AX5. I'm not super familiar with the AX5, but the AX15 that the 4.0 manuals use is a very good transmission. An 88 automatic would have been a...Chrysler A904 I think? Anyway, don't fret about the quality of your transmission. Some are better than others, but I don't think any of the XJ's trannies were truly bad.
The different transmissions have different gear ratios of their own necessitating different rear axle gear ratios. And unless the torque converter of an auto is locked, not all engine power is transferred directly through the transmission.
This calculator might be extremely handy for you. http://www.manoian.net/jeep/gear_ratio_calculator.html
I don't have the exact dimensions of the 2.5 and no time to do the math right now anyway, but I'd say that your ideal cruising RPM should be at 2500; probably about 3000 RPM more likely. Here's another link you might find useful that I just scrounged-up for you: http://www.jedi.com/obiwan/jeep/2.5Lpower.html
This is just based on my quick educated guesswork, so I might be off a little, but if I were you, I think regearing to 4.56 give or take. Maybe even 4.88 if your big into wheeling.
Asking the YJ guys might get you some more wisdom as many of them had/have your 2.5 and AX5 drivetrain.
P.S. Listing all other mods you're running can be very helpful.