OK, I have an engineering degree and can't answer all the above off the top of my head, but here's a start.

Allen heads be they square topped or buttons need access from the end, hex's can be got at from the side. The bigger the hex (external is biggest), the more torque (turning force) you can apply before you break something. You can replace most with standard Allen heads, but the manufacturer is thinking about control on a production line and so picks what works best for him.

Sizes (M4, M5 , M6) etc. are the size of the hole/rod you start with. The pitch is the angle of the spiral. An M6x1.5 will take a bigger load than an M4x1.5 simply because it's thicker. Having finer pitch means more spirals over a given length, hence more contact area and more grip. It also vibrates loose at different frequencies. An M10x1.0 is typically a stronger joint than an M10x1.5, but will fit in a space where you can't fit the M12x1.5. Fine threads are easier to wreck by rough assembly, hence the standards tell you to try and use course pitch if you can. If everything on the bike was M10x1.5 it'd be rather heavy, hence the size variation! The only people who built a vehicle you can take to bits with one spanner worked for the Russian Army!

I hope you are NOT changing ALL your bolts to stainless. Stainless is fine when properly lubed on assembly and used where ultimate strength is not an issue. OK, replace the engine cover bolts with copper-slipped stainless, but think twice about the luggage rack and don't even think once about the brake calliper bolts! If in doubt fit new standard bolts every couple of years as they start to look nasty.

A washer can do two things properly and one as a bodge. It spreads the load to prevent the head pulling through and acts as a spring to keep the bolt in tension and prevent the head turning through vibration. It's shape decides how well it does which. As a bodge it fills an oversize hole. The type of washer needed depends on the load, fastener load, vibration frequency etc. For Yamaha it is actually worth testing every component to see if it needs a flat washer, nyloc, spring washer, wavy washer etc. If they save 2p on every engine by using a standard nut rather than nyloc or wavy washer it soon adds up. Production engineers and design engineers actually come to blows over one wanting a single gun-on nyloc and the other wanting wavy washered and wired!

UNC and UNF are imperial/US sizes where the design is set by different parameters. Metric is the world standard. Vehicle wise everything after about 1990 should be metric. This means all fasteners are to designs held in Paris and designated as M (for metric), Size (in mm), x, pitch (as a ratio). The spanner and allen key sizes for each type are defined in the spec and there is a design book listing which you should pick first. The problem is that for years the US was clueless and had the manufacturing strength to simply ignore all standards and the Japanese big export market was the US where everyone had inch size tools. As a result you get abominations like an M10x1.3 bolt with a 7/8" AF flange head and built in Torx security bit hole! (That was on a Russian built valve for a US owned company, so we guessed if was a mistake in the translation!)

If you are worried:

Only use stainless if you are sure.
Replace like for like or go up (ie nyloc and washer replaces nut and spring washer).
If you do have weird sizes (fine pitch, Imperial/US mixed) get a thread gauge.
Never force a fastener.
Always use copperslip unless told not to.
Don't reuse old fasteners unless you are sure they did not stretch.

If you have a workshop available buy yourself a block of aluminium, a tap and a selection of bolts. Learn to feel when a thread is about to strip. This is way safer that having loose bolts or messing about with uncalibrated torque wrenches. I once took a torque meter round some UK workshops. The average uncalibrated torque wrench was 15% out. Vehicle fitters got within that by feel alone. They didn't like my idea that service instructions should get rid of the numbers and replace with Tight, Very Tight, ****** tight, ******* tight, ****** ******* tight etc. but we did add the word CALIBRATED

BTW, the best fastener engineer I know is a Woman. This probably shows who was listening in Uni and who was thinking about Trucks/bikes/planes etc.

Andy