The 3 3/4" intakes are fine. You will most likely find you keep 2 closed all the way, and fine tune the temp with the last one (thats why you only leave them all open during initial startup, and why most people just put removable caps on those two).
For the nipples, go to the hardware store and get "black iron pipe nipples". These are used for gas lines, and usually in the area where the black iron pipe is.
Don't use copper, galvanized, or PVC. Galvanized is typically just zinc unless it's really old, but may be better to be safe.
Or you could just leave the drilled holes and cover them with magnets like some people do.
Ahh, the beauty of improvising and the UDS.
-elbows deep in someone else's misery.