Just a few questions
 

I've had my 98 F150 4.6 2wd Windsor for a month or so, it has no cats but all the 02 sensor's and a rough idle. It's not so bad at low RPM's but really noticeable when I tried it on the highway. Really like this truck and want to fix it have about 160,000 just had plugs done, didn't have money for wires and new air filter. Any suggestions on what to look into next?

You must have codes set.
Did you look for them with a Scanner?
The missing cats will set codes for both sides.
With the CEL on you can't see any additional code issues.
Looking from the outside is now just guessing.
Good luck.

They ran the scan tool on it at inspection, they said it was only for the cats, I wouldn't even know if my CEL came on again because the guy that had it before me must have taken the bulb out. If I check for codes again will it display more than one code at a time?

I don't know what your position is on taking parts/functions off a vehicle but it should not be done.
If your in an area that includes emission inspection the truck won't pass even if only the CEL lamp is out and no codes are set.
.
You still need to look at live data for an out of limits indicator such as the long term fuel trim tables.
These tables should not be shifted much over 10% rich or lean without beginning to affect idle smoothness
The IAC and throttle body may need cleaning. This would affect idle air into the motor without setting a code.
If the CEL does not light at ignition to run for dash check out, replace the lamp.
Put a new set of cats back on and clean up the system and it will run smooth like it was designed to do.
This getto way of trying to get around things is not the answer.
It cannot be done on the later vehicles that are getting so complex you cannot work on them much longer.
Think pulse width modulated fuel injectors are neat, try pulse width modulated fuel pumps. There here now along with the control circuit that drives them.

Good luck.

Better find some.

The 4.6 engine tend to clog up the egr passages. You may also need to remove the throttle body and clean out those passages. But you should be getting an egr code if that is the case.