It seems to be rubbing somewhere, but the cover doesn't have any alignment dowels or anyway to adjust it. Is there anything I can do to ensure proper alignment?
A couple of those long cover bolts can get started kind of screwy. Are you sure you're getting those bolts in right? I've heard of people finding epoxy stuck inside the rotor bore that causes the rotor to wobble. You could have a bent crankshaft.
You can get couple long bolts (4-5 inch) with correct thread pitch, cut their heads off. Start them into the engine case, now you can use those bolts as a guide for your stator cover. It is obvious it's rubbing, you just need to find where.