The cam out feature to prevent over torquing by design in the Phillips Screws is a false claim.  To the contrary the design was intended to allow the screw to be installed and removed multiple times without damage to the screw head.  The cam feature of the design was one to remove debris which may be in the slots.  Search for Patent 2046847. 

Here is a snippet from the patent.  "Moreover, by reason of the perfect fit between the driver and the screw, the screws may be driven and removed innumerable times without the slightest indication of mutilation to the head. This highly desirable feature is made possible by the firm contact of all the angular faces of the driver into the corresponding angular faces of the recess formed at many difierent equidistant points around the longitudinal center line of both the screw and the driver. Thus, is provided many times as much gripping area as is provided in the slotted screw. This obviously, gives greatly increased strength and torsion with the result that my screws can be driven into material which slotted-head screws could not be made to penetrate.?

I'm not sure I'd use loctite...  maybe the low strength small screw purple or whatever color it is....  blue might be ok too.

If nothing else, using anti-sieze (sparingly), grease (sparingly), or even just a drop of oil on the threads is a very good idea.  Will allow for proper torque and the biggest reason the screws get stuck is galvanic corrosion. 

Lube, oil, grease, anti-seize on case screws is something I have never heard of, but it would definitely delay any galvanic corrosion.  Under normal conditions we are not worried about removal of case screws, that is when an impact driver comes into use.  However, we are concerned with proper torque, positive retention, and prevention of loosening.  As many have stated here hand tighten of case screw should be adequate, I do not recall ever using a torque wrench on Phillips screws.

Great thread, as I will be doing this step soon in re-assembly of my IT175E project engine.

I use anti-seize on my bolts,screws and spark plugs loctite on a Harley. As MarkT says just a little bit 

I have an original Yamaha tool kit, can I assume then the screwdrivers in the kit would be JIS type drivers

I want to thank everyone  for the replies. As far as drivers, I have the Vessel set of jis drivers and agree that they are a great tool. About half of the crank case cover bolts had stripped heads on them. It is not surprising what you might find on these old bikes.

Rodney

Is it weird that my case missmatched (original left had a big ass hole from bike being dropped from a forklift into a dumpster onto its shifter) halves were sealed with a very very very light coat  (some spots probably got none) of permatex aircraft sealer (the black goop), and they havent leaked a at all after buttoning it all back together? Reading various forum posts about this makes me think it should be leaking like a siv.

Why would you think it would leak?

Permatex Aircraft Sealer #3 would probably be the best choice of the Aircraft Sealer line if you didn't use Yamabond or Permatex MotoSeal.

The more "paste-y" #2 aircraft might work too. #1 aircraft would be a bad idea.

(I had a friend glue a cylinder head on a MG with Permatex #1 Aircraft Sealer... it hardens and the head would not come off again, period. He ended up buying a junk yard engine we rebuilt. I don't know if it still is but back then it was labeled "permanent hardening" and it was! )

Permatex #2 or #3 is just really nasty stuff to clean off next time... and doesn't seem necessary since Auto Parts stores usually carry the "MotoSeal" these days.

Silicone seal is the worst stuff around gas... might seal for a while but will almost always start leaking.