FXR Transmissions
"I noticed I could wobble the engine side to side without the swingarm moving with it."
Wasn't sure whether you went with nylon bushings or a actual bearing kit in the swing arm but consider this;
If the top link is adjusted "neutral" so a mount bolt will drop in like it should, and you can push the engine transmission assembly laterally left to right (even a small distance) when riding, that top link is binding when it shifts one way or the other. That will transmit a LOT of vibes to the top rail of the frame.
The one thing aftermarket swing arm kits or even the FSM doesn't mention is the importance of the bushings/bearing being pressed in so they are a tight fit against the transmission standoff. Obviously they have to be spaced enough to mount the swing arm but there should be zero side play between the mount and the inner side of the bearings. If you can easily put the rear fork in place and line up the pivot shaft, it's too loose. It should tight enough where the swing arm will simply hang there by itself and have to be gently hammered into place to get the shaft in.
Not saying you don't have a wallowed hole and I could be wrong, but I have a feeling the "side play" you have at the pivot could be the main problem. But if you do end up pulling the trans case, you could get a thin bushing installed and reamed to make it correct. Most any machine shop should be able to do that.
I can appreciate your frustration. Bearings or nylon bushing will add some degree of vibration over the original rubber version.
Again, no matter what bushings or bearings are used, the transmission should be sandwiched snugly between the inner bearings of the swing arm, and the outer swing arm races should be sandwiched tight between the isolators and they should be the same between the isolator mounts.
Loosen the belt, but a piece of slick plastic (like a piece cutout of an oil bottle or anti-freeze jug) under the footprint of the tire. Jack it up enough to remove the lower shock bolts and swing them up out of the way. See how much play you have and where it is. Go from there.
There is an alternative fix for a wobbly shaft I have used many times on much heavier and more critical applications. I'll only explain that in a PM, if you decide the transmission bore is the culprit.










