You might want to make a brace between the muffler body and the bike frame out of some decently thick steel 3/8ths" strapping. Some of the bad vibrations is due to the muffler oscillating back and forth at certain engine speeds. If it's allowed to vibrate like that too long, it will break off the muffler studs and possibly break the cylinder.
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Disc Brakes are not an easy option for old bikes like this. If the brake pads are old and worn you should think about a new set, they're cantilevers, they'll be some of the cheapest parts to replace in this bike. Always clean the rim surface with rubbing alcohol before installing new brake pads/shoes. Also inspect the wheel's rim's braking surface for wear. You don't want to be riding on a pair of worn out alloy rims that have big brake shoe wear tracks in them, as they'll fail without warning and having your rims split explosively at speed would not be a lot of fun.