Got her running! The air cleaner is shot and it has the wrong plugs. I did a compression check and the the right cylinder only has 103 PSI average but the right has 139 PSI average. I had to adjust the throttle / choke linkage and governor linkage to get the carburetor to work correctly. At first it just turned over with noting so I shot some starter fluid down the throat and she came to life. I was expecting her to fire up then die but she didn't she stayed in there and the engine sounds good. I fired her up several times today and she came to life each time with out the starter fluid. Then I took her out and drove her around a little bit to see how the hydro worked and if the PTO would engage. All is fine.
I called my local parts house to see if they could get the air filter and as Smitty said parts are going to be hard to find. But I have found a site on line that is supposed to have parts for the tractor. That Yamaha is a really nice tractor and has held up well for as old and abused it is..
Now I get to work on a Chinese ATV to see why it won't start.