1- A little searching on the web should find a new breather tube. If not, definitely plug the hole in the housing.
2- The engine mount should slide on the rods and the bolts w/ jam nuts are to hold the rods solid in the tranny housing. The bolts are not fill holes. The plastic caps are removable so you can screw a short bolt in them to drive the pin out of tranny housing. It sounds like the engine mount ears are seized on the rods. Some Kroil, PB blaster, etc and patience should free them up.
3- I'll suggest replacing both wheel axle seals and tine shaft seals. If this is a PTO model there are two points to check oil level in the tranny and tine gear boxes. You can go to the troybilt site and download an owners manual. Until the seals are replaced be sure it has plenty of oil. If not it will get expensive to repair.
You have a good rugged machine. If properly repaired and maintained it will outlast you.
Mike

So I should tighten down those bolts and use the nut to lock them light that AND be able to move the assembly up and down while the rods stay put? Right now sometimes the rod stays put, sometimes the rod comes too.

That's correct. The rods have to be stationary and there's a flat on the rod for the bolt to contact so make sure it's positioned correctly for bolt contact. Put a liberal amount of antiseize on the rods and in the bores they go in. They can get rusted in real bad and if you ever have to remove the engine it's easier to remove the engine and mount from the tiller. There's a good chance the wheel hubs will be rusted to the axle real bad also. When you get them off to change the seals use the antiseize on them also. I had to drill holes thru the wheels and use a two jaw puller and my O/A torch to get mine off.
Mike

#1. You DO NOT want to plug the crankcase breather. That acts like a PCV in a car engine. You plug it and once the engine oil gets hot the crank case pressure will raise. If the pressure does not have somewhere to go. It will cause oil leaks around the crank shaft seals and blow by in the cylinder which will lead to oil burning.

Believe it or not. Excessive crank case pressure can actually cause a small engine to explode.

Sorry, Hippie, I should have been more explicit. I meant plug the hole in the air filter housing.
Mike

The threaded holes in the vertical pins (pic 2, the "shaft things"), can also receive bolts to hold a 3' grader blade assembly. Attachment is the two shafts, plus one bolt under the engine center (requires a large bushing). The blade can be set at 5 different angles, left tilt and right tilt.

Here's one:
http://i14.photobucket.com/albums/a318/amigatec/Tiller/Blade_03.jpg

I have one also, had used it to plow wet slush for years. It actually works, But last year I bought a 7' blade for my old Ford 641. That goes a little faster, Two tons+ versus a few hundred pounds.