Magnum intake drilling plate project

The 1/8 by 3 inch nipples are not national pipe thread they are MIP which is quite a bit smaller than the npt's.

You are confused about something here, I don't know what. If you are talking about INTERNAL diameter, pipe and pipe fittings does vary. NPT is always the same outside, and the thread is tapered, so there can be minor differences there. But the wall thickness can vary some. Also, common pipe you'll run across is "skedule 40" you can get sked 80 which is thicker and therefore much smaller ID.