Plugs and wires are the thing to look at for a felt miss. 30K is the normal interval on plugs, 60K on wires, cap and rotor. Look for corrosion where the wires connect to the cap terminals, any found and it's time to replace them. Mopar wires are date coded.

On the 99 4.0l, it will take a few misfires in a row, within a certain amount of time for the code to set, but it you were able to watch the misfire monitors with a scan tool, you can see which cylinder is misfiring. It may have set a one trip fault, for which the light won't come on. Also, misfire faults are disabled with less than 15% fuel level in the tank.

Fuel system supply restriction issues (Filter plugged) will usually feel like a sag or lack of power until you cut the throttle, when they first start. The fuel filter is built into the top of the pump module, and it is not a normal scheduled maintanance item. It should be replaced when a pump is changed. The pump module also has a large, fine mesh pickup screen

A intermittant injector can cause a single cylinder miss. Injector Circuit issues will usually throw an immediate code though. A plugged injector usually stays plugged once it happens, causing a consistant miss.

Hope this helps!