Funny, that was my first thought as I just put new mounts and flanges in my boat club's Old Port 26 launch under a Yanmar HJ4 to solve a vibration after having had the trans rebuilt last year, so I thought I had just had shaft alignment on the brain and ignored it.
While I didn't put any feelers in there on my A4, it slid in so well and seemed like nothing I had done should have changed it, so I just tightened it up. The previous owner did install a pillow bushing (somewhat sloppily) about mid shaft, and the cap was off as I was working on it so that might be involved.
One of the nice things about this Tartan is that the engine is midship so that you can easily see and touch almost every surface of it!
