I have a 98' plymoth breeze, 4 cyl, 2.4L and here's the problem:

While ideling, the rpm would rev up past 1, go down, rev up, and go down again. It sounds like someone is pushing on the gas pedel when in actuality no one is. This morning, I was between changing from reverse to drive and then it stalled! Thankfully it started up again.

Also, when I am driving on the highway, it would backfire almost, like the transmission was shot. Any suggestions? Could it be the spark plugs? The timing belt is new so it isn't that.

I am not familiar with your engine... but on my car this would be one of two things:
a) a dirty Mass Air flow (MAF) meter
b) a dirty idle control valve (ICV)

Both can be cleaned and lubricated relatively easily (if your car has them).

You haven't given enough information the backfiring. If it is true backfiring (unburnt gas explodes in the exhaust), then it will not be related to your transmission.

Items to check:

. Check for any Diagnostic Trouble Codes--AutoZone will do this for free.
. Check for spark at each plug.
. Install new spark plugs--exact brand and plug number that originally came with the car.
. Test/change ignition coil--AutoZone should be able to do this for free.
. Replace spark plug wires.
. Ensure all spark plug wires are seated properly on coil and plugs.
. Clean/replace Idle Control Valve.
. Install new fuel filter.