Try Eqing them differently from one and other.
That usually works. I had a similar problem and it worked for me.

There is more than one way to skin a cat!(kind of a sick saying huh?)
There are a few ideas that may get you the result you want.
It sounds like you could have some phase issues, so try the 180 flip and see what happens.

Also are you using fx? If you are that could be causing an issue.

You could also try to offset one track by a few frames.

Maybe mono the mix and pan inward until you get a good level, then go back to stereo and see if it sounds good.

Finally, if the studio gremlins win, you might consider dropping to one track and put a stereo chorus on it, or re-do the second track again.

It might be a good idea, after you get it right, to figure out why you had this problem in the first place so you can avoid it in the future.
Are you using a computer to record?(latency issues perhaps?)

Long live huge guitars!

thanks guys I''ll check out your tips!
Macmod

Ron, did you eq a specific frequency area or trial and error?
cheers,
Macmod

Dave Pensado, has one trick to deal with this if the issue is FX device. Use the grabber and move one track 7ms forward and the other 7ms backwards and you have a cool stereo sound, instead of using a reverb. But this is only a solution if it is a reverb unit causing the trouble.

Macmod
It was some what trial and error. basically I carved out some low mids on one side and then take a listen in sterio. I just try to make them sound different
so they don't interact with one and other.

Macmod. It is probably a good idea to stay away from eq's as much as possible. I always look at eqing as a last resort. Particularly if you have cheap eq's. If your guitars are dissapearing in mono I would bet money that eqing won't fix it. What is happening here is that while audible in stereo the guitars cancell each other out when combined. This will be occurring at certain frequencies, as I'm sure that at least some part of the guitar remains audible. I don't proclaim to be an expert on phase, but I don't see any other way this could happen to you.
Eq's work by disrupting phase. In that context an eq might help, but I would try other means to solve things first.
one last thing. you could find the cleanest of the two takes, and copy the track. Then offset the track in small increments until the sound gets bigger. 0 to 5 ms. As the offset increases you will notice kind of a flangy sound you might not like. Apply fx to taste.