But my basic mechanical experience is limited, so knowledge like when to use the various goos such as grease, antiseize, loctite, etc is lacking.
That is a bit like asking what brand of beer do you prefer - you will get a lot of different answers and some heated opinions. The same goes with motor oil.
Here is my dogma:
In general whenever you assemble an engine it doesn't hurt to dunk anything that moves or touches anything that moves in engine oil. I do not use 'Lubriplate' or other engine assembly greases as I think they cause more problems then they are worth - although Pete Roper swears by a Penrite product not available here and I trust his opinion as I do John's.
I spin the oil pump up (chain off) using an electric drill with a suitable socket and check that oil is reaching the rockers before I install the chain. Then I know that I have oil on all the critical surfaces and I won't be spinning the engine dry.
Antiseize is great stuff and I use it on virtually all threads with the exception of things that I Loctite. Be aware there are two versions: one copper based (a.k.a 'Copaslip') and a nickel based one. The copper based one is for steel on steel only. The nickel based one is for everything so that is the one I buy. If you use Copaslip on steel into aluminum it may seize. Shame as I think the copper looks nice.
I think in most cases any non-hardening sealer will do - gaskets need to move as things heat up and cool down. Everyone has their favourite: some people swear by Hylomar, others Indian Head Shellac etc.
In general I use Permatex Hi-Tack Spray because it is easy to use, easy to get hold of and clean up and lets me position the gasket. On the base, sump and valve cover gaskets I spray one side and grease the other so that I can, hopefully, reuse them.
Any decent wheel bearing grease will do. For certain applications I like to use Mobil 1 synthetic grease as it does not wash off with water and is friendly to rubber.
No fancy sealant is going to help you if your rings are shot, your crankcase breather is stuck closed, the surfaces you want to seal are not flat or the bolts are not torqued correctly.
In general I do not like using silicone/RTV as it is messy and may go places I don't want it to go like oil ways. I do use High temp silicone on the exhaust flange in place of the normal gasket but I put a bead on the pipe, let it dry and then assemble it.
Loctite is a godsend if used correctly. DO clean the threads with their cleaner or brake clean before hand. Do not apply copious amounts - a drop is all that is needed. Anything more than the low strength (blue) version will need heat to break the bond. Use it only on bolts where there is no mechanical lock and you are worried about it coming apart. I use the red stuff (high strength) on the clutch assembly bolts (which are one time use) and Loctite PRT on the bolts holding the rear main crank carrier. These bolts go through to the crankcase and need to be sealed against oil.
Do not use their new 'Loctite' in gel form - it looks like a lipstick container. We used this at work and discovered that it was useless. It may have been a bad batch but I don't want to experiment.
Loctite has a new anerobic flange sealant that I would like to try as where it is not required it should just wipe away.
Carroll Smith's books, although not specific to motorbikes, are very good at explaining why things are engineered the way they are.