So, I believe the individual bays are the number of Spaces – if I’m wrong, please tell me! The weapons layout will be;
Unfortunately, you are wrong here, every individual weapon counts against the weapon slots, including AMS. So your layout currently looks a bit like this:
Nose/Aft: 36 weapons
Fore Sides: 41 weapons
Aft Sides: 40 weapons
and each location requires additional fire control tonnage.
As for the rest, there are a couple things missing or not quite adding up.
First, based entirely on what you posted, you are short 440 tons, I suspect these are intended to go to Heat Sinks, but you didn't mention it anywhere.
Second, your first portion's sum is missing a couple items, notably the crew quarters and the jump sail (at least, together, these add up to the missing value). Also notably, you mention you are using 2nd class officer's quarters, which would be 7 tons each, rather than the calculated 10 tons, and this would probably decrease the crew quarters to 5 ton quarters, overall saving you some mass. I suspect this oversight was due to the intention of adding in gunners when you figured out how many you'd need.
Lastly, gunners will need officers too, and at the same ratio as the standard crew.
Very lastly, I'll note: I'm assuming the formulas you are providing are correct. I've based my observations entirely on what you've put before us.