If the pipe isn't leaking now it shouldn't leak when you change the mufflers.
As far as the rear main seal, I wouldn't go in there just for that unless it's leaking badly. To get at it you have to remove the H-pipe, driveshaft, trans, bellhousing, clutch and flywheel. If your going to do all that it's best to do it when you need to replace the clutch so you don't have to do it twice. It's not too difficult of a job, just time consuming.
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