The gasket size will affect the quench, or squish, on the engine. The system is designed to have the pistons move to a certain distance from the head, and messing with that by literally thousandths of an inch will change how the engine behaves. Personally, I don't understand the effects, I just know they are there, so I always try to get the right thickness on my gaskets. An engineer who specializes in this kind of thing might choose differently.
Loctite on head bolts is a no-no. Loctite is designed to change from a thread locker to a lubricant at high temperatures, which can cause some unexpected problems if you use it in high temperature locations. Find some moly lube at an auto store, or, failing that, a light coat of engine oil will work. Note that you need to use a different torque for oil than you do moly lube.
The MLS gaskets from SIP are made by Cometic, last I heard.
With the amount of material already removed from your setup - the pistons poking out the top of the block, etc, I'd definitely be switching to a metal head gasket. This isn't as easy as it sounds, as you'd probably need to pull the block, disassemble it, have it decked to a properly smooth roughness average (RA), and do the same with the head.
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