The clearance between the shaft and the manifold should be sufficient to keep the shaft from sticking, once it's moving freely. Keeping any kind of lube there when it's exposed to exhaust gas is pretty much of a lost cause. I like to duplicate all the parts in stainless steel, so there's less of a chance of the shaft and the manifold rusting together again. Once the shaft and flap valve is removed, using a chucking reamer in a cordless drill motor to precisely align the holes in the manifold and fabricating an oversized shaft is the "permanent" fix. Then make a new flap valve from a piece of 1/16" stainless steel and weld it to the shaft.
Jerry