The 2.5 is never going to be a speed demon. With that being said, my '99 2.5 / AX5 manual has acceptable performance with 31" tires.
Before throwing money at it, try shifting at around 3,200 RPM. Cruise at about 2,600 - 2,700 RPM. Jeep motors like a little RPM, and cruising in that range puts the engine at about the bottom of the usable power band. It gives you your best economy as well. Don't be afraid to spin the 2.5 up into the 4,500 RPM range or higher if you need to. You won't hurt it.
If you are running 31" tires or larger, then it's time to regear. 4.88 or my preference 5.13. Those ratios unlock all the potential there is in an SE with a manual transmission and are good on and off road up to about a 33" tire.
A healthy 2.5 responds well to a good tune up and a new O2 sensor.