Building (permanent) fixtures, especially frame size fixtures, is a skill in and of itself. I'd recommend trying to build a frame or two (or a bunch) without to see how that process works. It will better inform what you think you'll need it the fixture.

I'll also say that small irregularities in the first few frames are the norm, but having a small irregularity in your frame fixture will plague you for every bike you try to build on it.

You might be better served at this point with a flat reference point- even if it's just a surface ground piece of heavy channel.