(1) Just measure from the top of loop. This is not critical. Just get as close as you can because you will want to do a static test after the guides are located anyway. Put your reel seat and grip on first, then your tip top. Then tape your guides at the locations you have measured. Then put a reel on it and run your line through the guides. Flex the rod and see that the line path is correct.
(2) I typically don't use fighting butts. Others may be more familiar with these than me. I think all you need to do is make sure the blank is recessed in the grip enough to allow for the butt pin.