Hi I currently ride a decent spec 2003 mongoose full suspension but I find that the seat stay is slightly too narrow to run my maxxis high roller 2 2.3 tyre without it rubbing on the frame. In theory if I was able to find an appropriate length seat stay of I wider fitting even if it's not for my frame would I be able to swap out the seat stay and thus run my wide tyres? I don't see an issue as long as the seat stays are the same length and have the same shock fitting and attachment to chain stay.
EDIT: This answer supposed that the rear chainstay was welded to the frame. As such its inapplicable to this question, but being left for completeness.
That's a lot of work to cut off the old seat stays and weld in new ones. Plus you'd have to either cut them off an existing bike, or make the new seat stays up out of fresh steel.
Getting it done by an experienced and qualified framebuilder would be safest, but I'd be surprised if it was cheaper than a whole new bike.
The details of your suspension aren't obvious from your question - can you add a pic showing what you want to try?
Do you have rim or disk brakes? With rim brakes, the bosses will have to line up correctly, and with disk brakes it depends if your rear caliper is mounted to the seat or chain stay. Doubt that you have caliper brakes.
Remember, in 2003 a 2.1" tyre was huge. Noone anticipated tyres would become bigger-than-huge.
Your final option might be to trim your tyres a bit - removing some of the knobs might help fit in the frame. Or simply return to 2.2" or 2.1" tyres.
I'd strongly advise AGAINST trying to cold-set your frame with any sort of jack or puller - that is likely to crease the frame and decrease the structural strength required.