I doubt it is loctite, it might just be gasket sealer, I'd clean it off to make sure your torque readings are accurate, anything that puts a drag on the threads can result in your inadvertently overtorquing things. When I did mine I just put a light coat of OMC gasket sealer on the threads (this is mainly to prevent corrosion and make any future dis-assembly easier, as I'm in a salt water region). If you want to be really fussy you can use thread chaser to clean out the bolt holes in the cyl heads. When you do a head gasket or replace cyl heads like I did, this is a must, those head bolt threads get gunked up with junk because of the raw water cooling.
*HOWEVER* this is just my opinion, I don't have a current or past Merc manual or GM manual that covers the newer Vortecs, if I was working on one I'd follow exactly what they say.
As far as guide bolts, not a bad idea but you'd have to take your manifold bolt to a hardware store, buy a longer one, cut the head off and cut a groove in the end to remove it with a screwdriver after setting down the intake. The Vortec bolts go straight in so this might work, on the pre Vortec you can't because they are at an angle. There are guide pins on the gaskets and 2 holes in each cyl head to hold the gasket in place, so for that reason its easier on the Vortec than on the Pre Vortec.
The only reason to drain the water out with each change is if your water in the engine issue is not resolved. Once you fix this you should be good, run it for about an hr to burn off any residual moisture.
I did that because I couldn't take the engine apart right away, and had to pickle it for a few months before pulling it apart. When I did there was no rust in the cyls, or anywhere else for that matter surprisingly.