Welcome aboard! Coming along very nice, nice detail bits!
Bonefish Torpedo shutters - not confirmed, but she PROBABLY had the kit "spoon" style, so you are safe, and looking good with your linkage slot mods! AMP make a set that we think is better than the kit:
Paint: Robert has given you an excellent link. The early boats were launched in Measure 9 - all black (mostly flat, some gloss buts), and later repainted, and new boats launched with Measure 32: hull black, top and fairwater gray, some wavy bits.
ED: NOTE: I misread your post, so the following will sound pretty stupid, but I think it still fits:
Measure 32 was introduced in March 1944. Bonefish was commissioned May 1943, so she probably started with Measure 9. The launch pic at navsource and wikipedia show an even, dark, tone, def black! But she was also probably repainted later. If you are depicting her past march 44, you're safe with M32. Her 4th patrol was April-May 44, doubtful that she was repainted at this time (not enough time between the order and refit time and out for patrol). The earliest easily possible repaint would have been on return, before her 5th patrol (June to August). Speculation, but trying to fit in with known info. This pic showing her in Measure 32 black/gray is at navsource.org, and says "...Fremantle, Austraila, circa 1943 - 45" but we know it's AFTER 43 because of the M32 color.
Even tho Bonefish was repainted in dec 43, I think she would have been repainted in BLACK, because the boats were constantly painted, it was "nothing" to slap on some more paint. Cdr O'Kane of Tang noted how FAST his newly painted boat looked faded and chipped (a patrol). so even after rereading your post, i stand by the logic of the above. I'll try to dig up a visual for M32...
great wtuff, keep it up! Oh, sonar, wil see what I can find, I' sure some folks have done the sound heads and have some info...