When I rebuilt my 3 rib bigport 4age my machinist had to deck the block as it had pitting on it around the water galleries, I don't know how much it was decked but the pistons were sticking out of the block a little when assembled, felt by running my hand along the block.
I also had my head decked and am running a .8mm TRD head gasket.
I had no problem with valves hitting the head as one cam was 180 out when I first started the engine. It now runs fine(cams aligned) on 98 and the std JDM ECU.
I don't know how much compression it works out to be but it will be a fair bit from std.
If you want to raise compression don't used the cardboard head gasket that you get in the rebuild kits, a TRD metal one is ~$80
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