Sinclair's bridge is larger than the model's and his turbo lift shaft is nearly a third taller, so for what you are wanting to do, those plans were the best choice... specially if you decided to use the McMaster's bridge plans, which are about 14% larger than the original set plans.
So to get a bridge that is 14% larger into the Enterprise, I can see where having the Enterprise be about 14% larger as well would solve a ton of issues. And avoiding Casimiro's plans (which have the correct dimensions for the bridge dome and turbo lift shaft compared to the actual model) also side stepped issues that would have been a problem even after scaling up the overall dimensions. Plus Casimiro has done a better job on matching the original window placement, which again would be inconvenient (and best avoided).
You're doing a great job so far (better than those based on Joseph's plans, but I'm bias) and I look forward to seeing how this turns out. These types of projects are always my favorites to follow.