Allen,
The Fox 35 liner is very thin and can be distorted by a number of things that have already been described. For me the most frequent problems come from - muffler to tight; wrong size head bolts (with the stock head you can't normally use socket head bolts as the head diameter is just a little larger then the stock philips heads and distorts the liner they are tightened); hard mount pads - the fox mounts have a very slight angle to them that works well with wood mounts but if you use aluminum pads as you tighten down on the mount bolts it distorts the case and causes binding, I use 1/32 plywood shim under the engine to give some "crush" room, work for me).
In your case since it is binding outside the case first check for varnish if you have been using all castor fuel. This can be removed with a green Scotch Bright pad, be careful go slow and only were the varnish is, sometime you need to do the piston also. Just get the varnish off so the piston is free don't try to get to bare metal you will likely have no compression.
If varnish is not the problem and you want to lap it you can use white DuPont rubbing compound. Again, go slow and check the fit often, stop once it is free. Clean with hot water and detergent. As you assemble oil the parts with a light oil.
As for the stick in the bypass, you might consider, since you have the engine apart, cleaning the case and degreasing the bypass area then roughen it with some sand paper and putting JB Weld to fill about 1/2 the depth. This amounts to about 1/8 oz of JB Weld. When I did mine, I put it in the upper part of the bypass and laid the case on its side with the bypass facing down. The angle created by the mount lug lets the JBW flow out and cover the rest.
I think Bret has done it with the JBW also and might add some thoughts on his approach.
Best, DennisT