Well, either way, thanks Fred. In the end, I chose to leave the cargo and vehicle bay much as they are in practice, even if the geometry is a bit different. The Cargo bay, not counting the vehicle bay or the pylon storage, has the same carrying capacity as the original Plumeria. Pylon storage is not quite as big as it looks due to the need not to compromise the gained structural integrity. It's pretty much "pack stuff between the rubs and structural supports", and just happens to have enough room to store some more SSCC-XL or POMs there. Happy accident. Vehicle storage is greatly expanded.
I've also finished the main gun of the ship, which borrows a lot from the Fuji and also attempts to reconcile the massive range of the weapon (already reduced to match the Fuji) with the functional three light-second rule. Firing rates have also been brought up to match the Fuji's, and a new wider firing mode with the same volume and power as the 30 degree one has been added.
The bridge's art has also been finalized and put on the wiki.
The main things that need done before submission, some of which which I would welcome aid with, are:
Come up with ideas and articles for the different types of modular pod to make available for the ship, including a default one.
Get the article proofread and truncated. The additional rooms and detail have made the article double from 12 pages to 24 in a text editor.
Get the YSS Sakura II's plot and starship pages in order. Turns out that something's not quite right there, and it's making red links in my article.
If anyone has ideas, input, or revised text, please feel free to comment.
Edit: Made this Drop Pod as a default starting pod. Also added a "Sublight Speed on Pylon Engines Only" entry, so that GMs know how fast the ship can go if a nacelle is knocked out.
Split Drop Pod into the Plumeria Bay Pod and the Plumeria Drop Pod. The latter is standard and can increase the Plumeria's already existing vehicle compliment and make it directly accessible to Deck 5's occupants...
Fixed Sakura II page problem. Still pondering Pod types, maybe some sort of Captain's Yacht or small parasitic escort.
The last thing I technically need to do, though, is to find a way to truncate the Plumeria 2E's page.