Hello. I am new guy that hasn't ridden a motorcycle in over 35 years until I bought this 125cc Enduro. After spending hours on research and going over most of the bike sorting out a few gremlins I could use some advice on a couple things.
1. Can the mica deposits on the starter, alternator at the brushes be easily removed? Do they hinder performance?
2. It also has an oil leak in this same area. But, just few drops. Is the oil seal in there difficult to remove and replace by just removing the electronic block that holds all the wires etc.?
My mechanical abilities are OK. My biggest fear is fear of messing something up. Thanks.

Welcome from NZ. Any armatures on similar i've machined i've just used a hacksaw blade but by memory i had to narrow it a little & scratch away to get it below the armature level after the machining.
Been a long time & not particularly talking your model.
So far as cleaning goes i just use degreaser & a light water blast then blow it off. Not sure the dust afects the performance though.
I wonder if there's lower quality brushes that shed a lot of carbon.
I'm mostly used the starter motors on Quad bikes & had one lot of brushes the got used up real fast compared to the next lot.
Others may have a better method for sure.
Talking oil drips. If it's the left crank seal in behind there & she's running ok i'd leave it for now. At least the seal is geting a bit of fuel/oil lube.
To replace it you need the correct puller to be safe. Here's an example but there'll be heaps on ebay.
www.cmsnl.com/products/pullerarmature-iso_9089001111/



www.google.com/search?client=firefox-b-d...vid:pn9yTlMLAR4,st:0

Greetings from Tennessee 

Bike has 1500 original miles. Will pull the (re-sealed) case cover periodically to check for oil. FYI, the oil pump still has the original setting - paint still there.

Inner cover doesn't have a gasket & could possibly even have a little notch along the bottom edge to let it breath--or something--but i could be wrong on that point!!.
But anyway, if you pull that inner cover be very careful not to loose item #3 in the second link that fits in the inner cover in first link.
It stops the chain firing stuff through onto the generator in your case or flywheel in my case--my magneto bike. Confused--i haven't even started haha.

www.cmsnl.com/yamaha-at3-1972-1973-usa_m.../partslist/B-04.html
www.cmsnl.com/yamaha-at3-1972-1973-usa_m.../partslist/A-05.html