The Ecm has two fuses, one for the Quad driver, (TBI inj & EGR solenoid & cannister solenoid), the other fuse for its memory.
As the engine gets older, it changes, just like we do. It learns the engine conditions and adjusts for wear. It retains this in memory.
Now, since you've replaced a missing fuse, it's running better because it remembered. But now, it has run-on. My suggestion is to buy a can of BG 44K Fuel Injector Cleaner and pour into less than 1/2 tank of fuel. Run to less than 1/4 tank and fill with good gas. This will remove any carbon deposits in the combustion chamber.
The 2.8's are low on power, but run damn good.
You might try and leave the vehicle in Drive, shut off engine, then shift to Park after engine has stopped, this way there is still a load on the engine.