My 1998 ford explorer 4x4 while accelerating has a bumping feel

Check the transmission transfer.

Sounds likes trans problem common to the Explorer, try changing the transmission fluid (mercon V) and add an anti-shudder additive. Does it happen mostly between 45-60 mph?

A 3.0 manual transmission will fit on a 1998 Ford Probe vehicle. ---------------------------------------------------------------------------------
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did you replace on front also and maybe have sway bar checked..

if your are expeirencing tranny slippage your tranny is on its way out...its only a matter of time before it goes... you can ride it out until it goes or u can either replace it with one from ten junkyard or get it rebuild.

voltage regulator in alt gone bad..will strain battery

New plugs and wires?

Double check to make sure that you've got the routing and firing order right... if you have 2 switched, the car may still idle well but then pop and sputter on harder acceleration.

The next step would be to run some "Complete Fuel System Cleaner"... If that's the problem, you should see results within 20 miles or so.

try changing the tranny oil and pan filter

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if it was me i would check the shock mount at the top to make sure they are in good shape and checkout the tires to make sure you do not have a bad one or two and also check the stabilizer bar to make the bushings are not bad