Deck height

Ok, let me see if I can answer your questions.

2. Yes, to measure compressed thickness of your head gasket, the most accurate way is to get one like you plan to use and torque it down on the engine, then take it off and measure the thickness and diameter of the fire ring. (or save a used one if you have one just like that has already been compressed).

3. For volume above the piston at TDC; If you have flat tops, you can just measure how far down the piston is at TDC, and the diameter of the cylinder bore and calculate from there.

You can also use the water method with the cover plate as described in the compression check thread.

You could also try to do both to check for accuracy, but they should come out the same if done correctly.

4. I don't get how your bore is 3.95 when is should be 3.40, and you say that it's smaller. Isn't 3.95" bigger than 3.40"?

5. I usually just use the stock stroke numbers from the books to calculate swept volume, but if you don't think that your engine is "to the book" then find BDC and measure the depth of the piston in the bore at TDC & BDC, then take the difference.

6. I recommend the liquid method if you can't measure it easily. (It's much easier if it makes a perfect cylinder and no other "variations" to calculate with bore and depth). The liquid method accounts for everything in your engine, but is not practical to measure at BDC (the water tends to leak when you are trying to fill this much volume). You can just use the bore diameter that you measure at the top, I don't think a little wear will affect the results that much.