Actually, you’re right on track with your method, adapting is a major part of building, it’s what defines us. Cigar boxes are commonly crooked, so lots of times we have to find center & true everything off of that. But if everything in a build was perfect, this would get boring quick? Good luck with this one :) is this your 1st attempt at a bolt on neck?
I mostly build ukuleles where there’s a bridge or block that the strings tie to. Regardless of how square the neck is with the front of the box, that bridge or block has to be glued to the box in the right location so that the outermost strings are spaced equally from the edge of the fingerboard. I usually attach the neck and clamp the nut in place. Then I run a loop of fishing line over the nut and through the outer holes in the block. I can then find the correct location for the block by moving it around until the strings align with the neck properly.
There are a lot of places on a CBG where we might obsess with keeping things square when it really doesn’t matter functionally as long as it looks good. It’s often a mistake to assume the box is square, so be prepared to make your work fit the box rather than your square.
Hi, here is the way I line up my necks on CBG's.
I use a long straight piece of hardwood with centre marks at each end in the form of a saw cut. this is laid out on the neck, as shown, with a projection point where the centre of the bridge or the tailpiece will be. The straight edge is clamped to the neck/fingerboard, and at the tail end if needed, and I can then do the required marking and fitting.