RE: General port timing guidelines?
Another thought....
Lowering the cylinder by leaving out the base gasket and/or machining the block or cylinder base does several things besides raising the compression ratio. One, it DECREASES exhaust timing. Two, it INCREASES intake timing. Three, it brings about the possibility of the exhaust port not being opened completely by the piston.
Since your engine exhibits all three items, it makes me think that someone has lowered the cylinder....
AV8TOR