Thanks Martin, glad I can fix some of the gaps, since theres quiet a bit now that I get further into the kit. This kit is challenging if a single part is misaligned, theres tons of stuff that will also be off.
Aft flight deck support in place, test fitted using the overhead beam piece as a guide.

Fast forward a little bit. Here we found a issue with the flight deck support beams. Notice the port side piece next to the railing from the near platform. The beams are supposed to fit between these rails on both sides of the ship, but thats not working.

My solution was to cut out that side railing thats place next to the beam. Why would a rail be needed there anyways when the beam is there? Come on Merit. Heres what I did to the railings, with the port side finished, and the starboard side in progress. Once this was finished, the beam supports fit well.

Next on the fitment correction tab. A good reason why parts should be dry fitted beforehand. For this starboard forward 5/38 gallery, notice the tab sticking out instead of lining up with the wall (2nd to last porthole). To correct this, I decided to cut that size tab into the deck of the gallery. I thought it was a clever solution.

Wrong. Was too busy trying to get the tab to fit to notice the part lining up.

Solution was to cut out the rear tab, which I should have done instead of the front. Here's the piece now

And the new fitment. Much better! The port side gallery isn't as bad.

Also did a dry fit of the flight deck, which seems to fit very well. That was surprising.
