Lots of questions…. Whew! Your on the right path.
Zero decking the pistons will not be needed. However if you went that route with a set of KB-107’s & a older letter head which fall in around 72cc’s, you’ll have a 9.8-1 ratio with that .039 head gasket. In order to drop that .8 in ratio, you’ll need a pretty thick gasket.
Don’t zero deck it.
You’ll have no issues with a 1.88 or 2.02 valve and clearance. The OEM heads can take more lift. Don’t worry about how much lift you’ll need. The cams I listed will do the job. You don’t need to run closed chambered heads. Aftermarket heads are cut to run bigger valves, so they need to be matched.
Oddly enough, I just seen the new engine masters where they make 360-365 hp from a 5.9 Magnum. Those stock heads are a little better than stock LA heads. That engine is @ 9.0-1.
