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The first thing to is to quantify what you have, measure all the items carefully or take all the suspect items to somebody who can .
It is almost impossible that you have picked up incorrectly sized replacement parts.

No! I'll do a bit of research
Back, The output from the alternator comes out via the 2 black wires to the  rectifier/regulator, check your connections.
With a multi meter check you have continuity on the alternator windings.
If these steps prove  the connections are all good ,it points towards the regulator / rectifier being faulty.

See if you can find some replacements in stainless  ,headlight rims buy repro replacements.

New type bulbs e.g. LED or HID have a different focal length ,so you cannot "Plug and play", you need a different reflector.
Over here in the U.K. if this setup is found on a vehicle's annual test  it is a "Fail"

About $110 i would think, what has that to do with lacing a wheel ?
If you have the old wheel just take a picture of the lacing pattern before you strip the hub out

Well at least it is for auction , what do you think it will top out at?
I'm thinking $6k

1st thing is to check all your earths (grounds) are good , clean and tight.

I agree with the above

Why wont it idle?

Go to the local model shop and get some 2 part fuel proofer  , matt and gloss is available , over here we call it Aerocote
(UK).Spray a light coat over the finished paintwork, spilt fuel will then not affect the paint finish.

OK. if you know WOT is about right, then decide whether your rich or lean in the middle, from your description it sounds rich when hot, so the needle needs to dropped a couple of notches . Your right about it being the sum of the pilot and the main , but if it idles with around 1 turn out on the air screw the mid range only is your problem which is only controlled on the needle up to 75% throttle, after that it's main jet to fine tune again

That says to me It's rich to start with when cold.
Start by getting the main jet near enough, if it idles ok the move to looking at the needle and jet assembly,

Read this article,

http://www.3cyl.com/mraxl/aylor/heads/heads.htm

What do you think is down there ? Gasket material, the odd circlip, use compressed air line.

Before you strip a wheel take a picture of the lacing pattern .Start the re lacing by fitting the correct spokes to the inside and outside of the hub, once you have the first few spokes placed into the rim it all starts to fall in place, as i stated first as long as you have a picture of the lacing pattern you are safe.