I have a JCM900 head, and I agree, there's no low end. You need some kind of external EQ. Changing tubes might help, but I doubt it. You could try removing the mid and high boost, then raise the master volume on the amp.
IMHO the best thing you can do for situations like this is a Graphic EQ at least six band or more and work with it, you can add it to your loop or input, can give you a third channel in essence as well