why you don't copy your two pieces in a single program. so, like that you will be able to make your toolpath and see easily if your tool for one piece will touch the other piece.
i think it's the best way to do it to be sure that you won't touch the other piece. also, i think that if you copy all your program in an other one, your tool path will be transfer at the same time. if not, from he dimension of your pieces, it look like it's only a outside toolpath to cut the pieces. i mean, it doesn't look like a complex 3 axis surfacique piece, so the toolpath will certainly don't take very long to make again.
good luck with mastercam and your router
Pascal "Le_KiD" Leclerc
i hope you will be able to understand my poor english