with that broken stud, do you have access to a mig welder ?
you could weld a nut to the stud, and undo it, the heat helps to break the rust seal
if you get stuck i can do it for you, but i'm from Brighton.
or do you have a gas torch ?
heat the stud up with the gas torch, then push an old candle against the stud, the heat will melt the wax, and it usually penetrates down the stud and the threads
then you can undo it with a pair of pliers
what i would do with the side cover screws is get a large round flat punch, around the same size as the screw head.
put the punch onto the head of the screw then give each one a firm tap with a hammer, it flattens the head off,
then find the correct sized screwdriver and give that a tap into the head of the screw.
this usually gives you enough grip to be able to undo it.
some valve grinding paste on the end of the screwdriver help it grip too.
you should be able to buy the replacement screw kit cheap, like this-
50 NEW Yamaha 6mm Case Screws AT1 CT1 DT1 RT1 JT1 GT80 | eBay
check your measurements against his.
another set, but dearer
NEW Yamaha 6mm Case Screw SET GT1 GT80 YZ80 | eBay
otherwise there is a seller on Ebay from QLD,that has some nice marine grade stainless screws too, he is pretty cheap
MARINE m6 screws | eBay
the piston look old and worn, the bore would have worn a little too.
if you tried honing it out, there might be too much clearance for the new piston and rings
i would bore the cylinder out to the next oversize, and get a new piston/rings, bearings, gudgeon,clips etc
i can give you a number of the guy that does my 2 stroke stuff, he is at Richmond.
a rebore will cost you about $50, you need to give him the new piston,rings and cylinder
and he usually take a day or so to do it.