There are a couple books out there on blueprinting. I have this one:
The Step-By-Step Guide to Engine Blueprinting: Practical Methods for Racing and RebuildingUnfortunately, a lot of the specific blueprinting techniques in it are sort of aimed at a Ford/Chevy/etc V8, but it's still some good food for thought.
This one I was just looking at the first few pages on, looks V8-oriented although perhaps could also be good:
Pro Engine BlueprintingOne thing I'd like to blueprint very much when it comes time to rebuild my Rabbit GTD autocrosser is it's cylinder to cylinder piston projection (and cylinder to cylinder compression ratio.) I think that could go a long way towards making the diesel run a lot more smoothly. Someday, perhaps next time you have your cylinder head off, try measuing all your piston projections. I was shocked to find how much piston projection varied across all cylinders. It was a little bit better on dad's 1.6D (which has a professional "vanilla" rebuild), but a far cry from exactly equal across all cylinders.