big are you making sure everything is the same? The tension on the screws is key to getting consistent accuracy. Next time you tighten everything up make marks on the screws and their mating surfaces (the stock, the trigger assembly etc) and you shouldnt see any appreciable difference. A difference of 2"-3" IS excessive if you ask me. My old Wolverine wouldnt shift one iota and that included my removal of the scope. But I always returned the screws too exactly the same point each time and my scope was mounted with a quality Warne quick detachable system.

I wouldnt want to do the same "complete dis-assembly" of my centerfires and expect them to return to zero. But the much larger, less stressed and more forgiving components in the modern in-line should allow you to do such. Afterall you MUST dis-assemble them to properly clean them. (Unless you have an Encore or Omega!)

Good luck,
RA