If you are going to have to split the cases to repair the blown second gear I would go ahead and check the cylinder taper and if still within spec I'd hone the cylinders and re ring them. If to much taper then a re-boar to the next larger size pistons and rings.
Now on the other hand if the trans can be repaired without splitting cases and I was trying to cut down my repair cost, I think I would run the engine with the same rings. I think it all depends on how much you want to put into this bike and is it a keeper.