My advice if you're rebuilding the engine to include boring the cylinders, pistons and crank to match, would be to purchase a complete rotating assembly for the motor. If your budget allows. Several reputable Pontiac suppliers sell those assemblies including Kens Machine Shop
, Kauffman Racing
, Pacific Performance Racing (PPR)
, and others. I bought mine off ebay from CNC Motorsports
and it's a solid performance assembly.
As for clearances, they are available in the Pontiac service manual (you should definitely have one of these for any resto... cheap to buy on ebay) and more performance oriented info is available in Jim Hand's book "http://www.amazon.com/How-Build-Performance-Pontiac-Design/dp/1884089674/ref=sr_1_1?ie=UTF8&qid=1328055783&sr=8-1s" , another "MUST HAVE" resource for building a great motor that costs less than $20. Specific optimal clearance numbers will depend upon the equipment you're using, oil your running and vehicle usage (street/strip, race only, street only, or any combo of the above).
Most engine "rebuild kits" are a set of gaskets and such, if you're replacing hardware you will likely need multiple items in order to get the job done, i.e., a rotating assembly, gasket kit, and any other hardware items you want for the build (distributor, head studs, cam, rockers, lifters, etc...).
Some basic engine info is available on P-Dude's website
, original stroke for a 400 was 3.75 with a 4.12 piston and 6.625 rod. Best bet is to get an entire kit if it fits your budget, if not, you'll need to use stock parts. No worries though, you can find most of those parts either completely reconditioned or in a condition that your local machine shop can work for a minimal charge. These parts can be found on the for sale section of this forum
and at the PY forum
Your challenge is to decide what your real goals are, and how much you have to spend.
If you have more specific questions, please ask. There are a lot of very knowledgeable folks here that have been through most of this before (I'm not one of them, but I have benefitted from their advice!). Good luck with your project.
And I agree with Rukee, if you're starting over -- STROKE IT!