Streets isn't being facetious here. You're asking the question of the wrong folks. It's not that someone here can't or won't give you an answer - it's just that answers from us don't do a darn thing for the quallity of your engine build. If you gave an engine to someone to build, and you have to ask those questions here, you gave the engine to the wrong guy.

1. Valve clearance is the builder's responsibility. If he's competent, he MUST measure it, and if there is inadequate clearance, fly cut the pistons to fix it. If your builder doesn't know the answer, grab your parts and run. (This applies to every other clearance in the engine, by the way.)

2. Compression ratio with a given set of parts isn't difficult to calculate. If you builder can't or won't answer this question, grab your parts and run.

3.a. The manifold won't need to be shaved unless the heads have been milled. Any competent builder knows how much to shave off an intake manifold for each .001" of head mill. If he doesn't, grab your parts and run.

3.b. I can't imagine a situation where the headers need to be cut down. They only mate to one head surface.