You are worrying too much about internal tolarances... everybody strips and ano's the entire gun. I've done lots of paintball guns, and all of them were completely stripped and re-ano'd with no ill effects (sometimes more than once).
The one item I don't strip and re-ano in the bore of a two-piece barrel. Just get some rubber corks from Lowes or where ever and plug the front and back protecting that critical bore. Don't worry about the breach, ram tubes, regulators, etc.
As for ano'ing only a few parts at a time, I highly recommend all the parts be ano'd together and dyed together so that the color and look comes out the same.
As for ano'ing small parts and large parts, I suggest getting a rectifier that is capable of supplying enough power to do your largest batch. I found the 10A power source the perfect size for paintball guns.
For smaller parts, just add a sacrificial hunk of aluminum in with the batch so that the current can be spread out over a larger area, and therefor more controllable.
Hope that helps.
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