So my service engine soon light keeps coming on and going off. It is usually affected by RPM but it is not consistent. Sometimes, its on at idle and goes away with throttle and sometimes its on while cruising and goes away when I let off the throttle. I just changed the oil and the level is good. The tranny fluid is above the add line. Could it be the fuel filter? I thought that would bring on "water in fuel" light if it gets clogged? What are your suggestions?

its probably either the egr valve[if you have one]and or vac switch acting up or TPS giving problems if TCL is hunting too. Maybe VAC pump is toast?
I got both problems on my 89 too, I blocked EGR, and pulled the TPS connector,was helluvalot cheaper than replacing both.
SES light is still intermittent after pulling the TPS but i dont care, truck works fine since.

Is there any testing I can do to trouble shoot those things? (EGR, TPS, Vac pump?)

to check the vac pump,pull the pump line at the soleniod with engine running,and check for suction. you can check the egr by taking it off and looking for proper working , valve should be closed and open when vac applied. You can eliminate the thing by putting a solid steel core gasket between the intake and EGR, and leave the vac lines in place. your ses light wont come on with that.
i dont know how to test the TPS.

Other causes for ses light is low oil pressure , overheating and alternator trouble

If you have a repair manual or access to one, you could short 2 pins in the diagnostic connector with the key in run position. The OBD system will then flash a code with the service engine soon light. Any decent repair manual will have a list of codes and what they represent. Details of which pins to short and how to read the codes should be in the repair manual. Good luck.

You might check at Autozone. They can check codes on 1996 and later. They may also be able to check earlier vehicle codes if they have someone who knows how.

Well, the light is never on unless the engine is running. Will it still flash the code? BTW, oil pressure is high, and the light will come on when its cold so it can't be over heating. I guess I'll check the vacuum and egr. Even thought I'm not quite sure where they are.

Codes are stored in the CPU after the event happens. It will remain in memory for 50 Key starts.