So I have a 2004 Cavalier base and have many parts from my 98 including the door lock stuff and everything for electric windows. I was wondering if you can easily swap it or would I have to completely redo the wiring?

Short Answer:
No. Complete re haul.

The door locks work on a J work threw the BCM/PCM. Since the 98 is just one system it wont match up to the 2000-2005 BCM system.

If you acquired the entire wiring from a 2000+ from the BCM/ inner fuse panel back then you could.

Or do what I did and install power windows as if it were stock by just running your own wire to stock parts (Switch/motors).

So could I just wire the switches to a power when ignition is on and ground and same with motors to windows so it seems factory?

Yea basically that's what I did with mine.
My car came with a sunroof but no power windows, which the sunroof and power windows share a 25 amp fuse/relay.
So I just tied into that circuit and ran it and a ground to the switches and all the rest of the wiring thru the doors.

If you don't have a sunroof then just make sure you have a inline fuse and then a relay to make sure you cant run the windows when the ignition is off.
the relay you could always branch off something silly like the wiper motor.