As you have probably figured out, the tank bushings for the MR250 are different than that of the CR250 because of wider tank. I have a set, but can't part with them as I sometimes use my MR tank for long rides, but usually use my CR tank (have to use MR seat with MR tank and CR seat with CR tank). I think you can find suitable rubber bushings if you look long enough. Do you have the metal inserts or are you looking for those too??
On all other parts you are looking for, they are interchangeable with the CR250. Obviously, you can buy inner tubes online or at any cycle store. The air filter can still be purchased at any Honda dealer, although I usually have to wait three days to pick it up after ordering. It is the same air filter as the 75-76 CR250. I haven't tried to buy a filter clamp, but think you can adapt large, thin radiator type clamp if you can find one. I've bought thin clamps from motorcycle stores, but never tried to buy one with a diamater large enough for the air filter, so I don't know. And you might still be able to order one from Honda, I'm not sure.
On the carb manifold, I bought an extra one on ebay and keep it as a spare. They come up fairly often. Again, same as the 75-76 CR manifold. There is a company that makes them now, but they are fancy and very expensive. Don't buy one for a 73-74 CR as those are different.
Fender straps might still be available. I don't even keep one on my bike. There is absolutely not need for it. The rear fender doesn't move and stays perfectly in place without it. But if you want one, you can find they regularly on e-bay. Same as the CR250 strap.
Air box cover is same as 75-76 CR. If you are talking about the top of the box, just leave it off and rejet the carb a bit. You'll get a bit more power that way. If you are talking about the side cover, you'll want to find on on e-bay or somewhere else, but they are out there quite often (usually with entire airbox). The top of the MR airbox is different than the CR, but the side cover is the same.
On the shift lever, any lever from any year Honday CR 125 or 250 will bolt on. Splines are all the same. However, you'll find that most year's lever probably stick out from the crankcase more than you like. I've ridden with several no problem. But if you find any shift lever from a 73-76 CR, it will be a perfect fit. Those are aluminum rather than the steel one that came on the MR. My MR lever got bent pretty bad in a wreck, so I bought an aluminum CR lever or sometimes use a folding lever from another year Honda.
For many OEM or aftermarket parts, try
www.Re-mx.com Also there are several other sites that may have parts that will work.
Good luck.