Odd that you felt the aluminum temps were lower than the silver solder temps - I used common copper pipe soldering and flux, with a melting point of about 400C.
I have some aluminum solder for brazing - it doesn't melt until well over 600C. Had no issues at all with the silver solder on the OEM tubes - just have to make sure that they are scrubbed clean and properly fluxed, though, or the solder won't stick.
Hylomar works fine, but I'm a convert to the more easily obtained Yamabond now. As others have said, technically you shouldn't need it with the base o ring cylinders, though I suppose you could CAREFULLY put a VERY light amount on areas that are not going to be near the O-rings or cause excess sealant to squeeze into the O-ring's groove.
Definitely no goop on the head gasket - you'll notice they are slightly asymmetrical with respect to the lower 6oclock stud hole and the pushrod tubes - they will only go on one way, or else it is likely that the headgasket will be rubbing on the pushrod when the engine is assembled and running.