The tires are still used on compact tractors and it looks like you can get them from ebay suppliers for about $150-$170 for a set of two. I'm sure suppliers like M.E Miller would have them as well.
Miller Tire 5.00-12
For the muffler just get some steel pipe with the same thread size and you can adapt pretty much any muffler you want whether it be a thread on one or put a 90 turn and do a stack!
Ignition parts should be findable and if you get sick of the old points I would recommend a stens mega fire module. I put one on my old Allis and it works awesome and no messing around trying to get the old flywheel off to service the points which were way more expensive than the module and had a nice hot spark right away.
Air cleaner is something you may just have to put up a wanted add and keep an eye out on ebay and if you go to any swap meets or flea markets. They are around just have to find one if you want original. If you get it going before you find one you can always just get one of the little cone (K&N style) filters and put it on there so its safe to run until you find one.
Looks like a cool project though these old tractors do take some creativity some times. Hope this helps and good luck. Keep us updated as you go along and I'm sure people can help you along the way if you get stuck for ideas; it has helped me a few times.