You pointed out about the black funnel tops and I've indeed removed them from the 1941 plan. Yet while the 1942 and 1943 official models shows many parts in black instead of white (parts that were modifed over the earlier plans I suppose) the funnel tops themselves sport a diffferent, darker shade of black that also differently reflects light (it can be seen from the pictures I've linked), Also, the mast supporting the SC radar on the back of the second funnel shows it's lower part beign black while the upper part not, as it was supposed to be pained parly in black because of the funnel exhausts.
I've interpreted the pictures this way, yet I might still be wrong, what are you two cents about it?
I wouldn't take this picture for as a reference for coloring the drawing - note the black finish on other areas of the ship (half of the forward superstructure, the turrets, etc), which to me (on close inspection) looks to be the same shade as the other parts. Who knows why the model was colored differently - like you said, it might just be areas that were slightly modified or re-dimensioned. Again, I'm always a bit wary of using models for this sort of thing. Models are good if you're having trouble wrapping your head around a confusing amidships AA arrangement, or weirdly-shaped deck, but I wouldn't use them as a "be all to end all" reference. Keep in mind that the yard would likely end up modifying the design anyway.
Now that the searchlight platform on the back of the FCT would have (probably) not been used for that purpose anymore, it would have been left opened or it would have been enclosed?
Good question... it likely would have been a semaphore platform (flag signals are still in use after all) and remained open.
The new antennaes would have still been fixed with brackets or with solid whip platforms?
Go with the solid platforms but look at the postwar Iowas for what they should look like - I don't think the current ones are really what you want.
Here are some photos of the Korean War-era Iowa for reference:
http://navsource.org/archives/01/061/016173r.jpg http://navsource.org/archives/01/061/016173o.jpg
Will respond in more depth later...