I've heard mixed opinions on decking the block, some say it causes compression issues cause you're lowering the deck height and too much you gotta start using gasket shims
I have heard about the FelPro gaskets being somewhat forgiving but even still i'm concerned about it not holding up more then maybe 50K miles, from what I can tell from closer examination of the OEM Gasket it was on the road to failing.. Fortunatley the fire ring areas on the block all look good so theres that..
Valid concern, but I would say that if you're taking off enough surface to affect the compression or need a shim then the block was in bad shape to begin with. Honestly, if you can clean up the trouble spots and seal your gasket correctly I would think you'd be ok, though I would defer to any more experienced advice.
Curious Question though.. What about using small amounts of JB Weld in the pitted areas to fill em in, and just using a razor blade and fine sand paper to make it flush with the rest of the block deck? I've read some places and seen a few YouTube videos saying that could help. I've had success with JB Weld in the past plugging a radiator hole more then 10 years ago thats still holding up to this date in our 85 E150, obviously this would be drastically different.
Oddly enough I had a similar thought, but I'm honestly unsure. Some anecdotal stories have JB Weld holding up for longer than the truck and others have it failing immediately and mucking up their engine. If I were desperate or had a spare car and enough money to replace the block if I were wrong I could see myself giving it a try. Definitely not my area of expertise.
Also one other note... I've noticed that 1 out of the 16 head bolt holes is deeper then the others, the one closest to the water pump on the passenger side of the block.. Does this hole go into a cooling passage in the block or something? I mean obviously with the heads on it shouldn't matter the bolts should all be same and all i'm just curious. I filled 15 of them with brake cleaner to clean em out each one took a couple seconds.. Spraying into that one however seemed like an eternity and never filled. (not worried about the coolant as i'm flushing that anyway)..
Can't say for sure because I don't have the manual for your year, but I'd say that it's very likely that bolt goes through a coolant passage. Which brings me to a piece of advice I picked up on those:
When a head bolt goes through a coolant passage you lightly coat it with some kind of sealant at the bottom third of the threads. The other half of this is that if you do something to one head bolt (oil, grease, sealant, teflon tape, etc) then you should do the same to all the other head bolts on that side. The reason for this is torque symmetry: if one bolt has sealant and the others don't then that one bolt will likely show a falsely higher torque reading when fully tightened so they won't exert even pressure on the head & gasket, meaning you have a higher chance of warping the head or allowing a leak depending on it's location.
TL : DR -> If you suspect a head bolt goes through coolant passage, seal it. Whatever you do to one bolt do to the other 7.