Dig,
I had the same challenge for my restoration. I must have put in and taken out my transom 15 times before I put a bit in my drill and began drilling! I ended up drilling the holes slightly larger than I needed, but did so straight through. The slightly larger bit allowed for any differences in how the original manufacturer drilled the holes and slammed the screws in and moved on. I used large SS washers on the exterior sealed up with 4200 to prevent the aluminum from caving in or becoming distorted, and all of this worked out just right, I had no issues. I think it might have been Watermann who told me not to overthink it just do what you need to, do the best you can, reseal a hole with spar if you need to and move on, the more fun parts of the project are coming up after this! He was exactly right, so I recommend the same for you.
Hope this helps, really coming along nicely! I wouldn't bother with sanding down the JB Weld by the way, looks great the way it is and will be completely covered anyway.
Frey