It should be pointed out that the shots we see of the shutllecraft in the flight bay on TOS are out of scale
. I've done composites of the shot with a more properly scaled shuttlecraft (based on my drawings) and the craft ends up taking a noticeable amount of more room. It's still manageable, but it is bigger.
I think figuring out the hangar deck is very much like when I was figuring out how large my shuttlecraft would come out to. You have to do some detective work and judge for yourself what information takes precedence. You also have to decide what you want to accomplish. For myself I wanted a shuttlecraft that could exist as a "real" vehicle. That meant I tried to reason what Jefferies initially intended and balance that with what we actually saw.
The drawings in TMoST are an okay starting point, but I wouldn't give them the final word. I'd have to see how consistent it was with what we saw onscreen and balance between the two. The FJ drawings I'd give less weight to because he diverged in so many things when drawing up those plans.
Personally I'd opt for extending the flight deck fore bulkhead forward a bit even underneath the pylons. I simply think that gives the area more flexibility. I could suggest that the are below the flight deck were simply maintenance shops and that storage was locate fore of the flight deck we saw. That would be one way.
This is what it would look like with a more properly sized shuttlecraft, albeit a class H which a bit longer than a Class F although the craft's height and width are the same.
This is a quick and dirty reference I threw together as a starting point for what I might do with the hangar area. Note I've also scaled up the Shuttlecraft to be better representative of actual size.