Check your squish area first. My friend blew his up above 8000 ft after peeling a gasket. There are some differences in the tolerances from the factory.
I have two layers out on my 99 SLP piped Mtn Max 700. I ride anywhere from 2200-10,000. So far no problems. I do run a splash or two of AV fuel in each tank.
I have over 10000 miles with power inc pipes at 600 foot elevation with no problems it doesn't affect your compession or squish enough to worry about it they are way safe from the factory