Do you have a flex coupling? That makes alignment less critical.

I would start by loosening the coupling a little and measuring the gap at multiple spots around the coupling - It should be consistent. Next, rotate the shaft, about 30 degrees at a time and measure the gap again. It should not change and should remain equal all the way around.

Next, I have a machinist's tool used for measuring if a workpiece is centered in a lathe. It's a dial indicator that has a pin that rests against the workpiece and shows the movement as the piece is turned. Make a bracket to hold that close to the shaft, turn the shaft and observe the movement.

A proper flex coupling (I have a Vetus type 6) makes this less critical. Also, your cutlass bearing needs to be in good condition. The Beta manual gives you the alignment specs.

When I did a refit in NZ a few years back I took the shaft to a machine shop where they put it on a lathe to measure how true it was. I was amazed to see that a 1-1/4 inch, three foot shaft could deflect from true with very light pressure. The machinist said that it was as true as you could get.

Aligning the shaft was one of my biggest concerns when I repowered. While it did take me a few hours to get it right it was easier than I had expected. I didn't add the flex coupling until a couple of years later. When I visited the Beta factory they strongly recommended the flex coupling but because I have a V drive transmission and couldn't see how to fit one at that time they provided stiffer engine mounts.

Best of luck.