I don't post very much, but this thread caught my eye.
I've been assembling engines for 30 yrs or more, and actually had a job doing final assembly for a machine shop.
In my experiences it is about patience. Let your silicone gasket maker material sit for a good 20-30 mins.
I had a few intake bolts with heads cutoff and a slot cut in them to use as guide dowels, it made life easier, i would put 1 in a back corner and 1 in the front opposite corner. After i had the bolts all in finger tight i used a screw driver to remove the homemade dowel pins.
If you are working in a tight engine compartment, or a truck thats higher than stock and the intake is a heavy cast iron piece,. The dowels really help.
I had two old head bolts i used when doing big block chevy head work, those old heads were heavy.