The bushing is flush with the surface. It's been taking so long that I actually bought a new alternator so I wouldn't have to do this again for some time.

I think you are saying the bushing in your case was only flush with the opening between the two bosses. Ouch.

I would have still pushed back the insert and ground off a mm of the boss.

Since the fore-aft position is set by the front boss, the back boss does not need to be precisely located.

The insert will pull forward out of the back boss onto the engine block and the bolt will pull the front boss tight against the engine block. The back boss sets the pitch and yaw not the fore-aft.

So for anybody else runs into that case you can do like I suggest: bump the insert aft and file/sand/grind off a bit of the front of the back boss.

So the problem turned out to be an e10 bolt I dropped during installation. It's wedged itself in such a way that I can't line up the alternator. I've tried to get it out with a 4 claw grabber. It wiggles but won't come out. I'm at a loss at this point.