If you install a new one, which I would recommend, have a look at the end of the crankshaft. If someone used an improper puller to remove the timing side crank bearing, it is possible that the end of the crank is damaged which in turn could potentially damage the quill.
Do you know if the timing cover is the one that came with the engine... as in matching numbers? Not knowing exactly how they were machined at the factory, it’s just a guess, but the hole for the quill (in the timing cover) may not be concentric with the crankshaft. No idea as to if or how far out they can be, but the timing covers were numbered for a reason. Perhaps someone else can expand on that or debunk the theory.