Talking about fuel upgrade? Can't help you there other than you may be upgrading fuel only to run rich. Talking about air upgrade? The 2.5L gets enough air, upgrades on a stock, naturally aspirated engine are a waste.
Many Jeepers, including myself, have found that the Jeep engines work best in 100% stock form (when they are naturally aspirated, non-stroked engines). Stock plugs, air, computer. The only upgrade I've heard good things about is the Bosch 4-hole injectors which are not relevant to your case.
for OJ, my YJ. 1993 Wrangler S 2.5L/AX-5/NP231, Spartan Locked Dana 30/open Dana 35 @ 4.10, 2.5" OME HD springs and Rancho RS5000 shocks, Barricade 9500 winch, custom front and rear bumpers, 136 amp alternator, 30" General Grabber AT2 tires.
1990 Yamaha TW200.
Jeep manuals? YJs, TJs, XJs, WJs, ZJs, parts, electrical, powertrain.