"Yes. I tried that approach and found the angle not friendly to the boxy shuttles, especially given the size of the opening for the elevator as seen from the flight deck shots."
If you uplift the shuttle from the hangar bay to the flight deck in the position the shuttle had when it was first boarded, it seems an angle less than 45° is possible to deliver it to the flight deck without the hull of the shuttle being scratched by the opening. I'm enclosing this shot just to illustrate
the ratio between shuttle width and shuttlepad diameter: http://tos.trekcore.com/gallery/albu..._Seven_020.JPG
It would, indeed, be a problem if the shuttle were uplifted with the bow first, already facing the clamshell space doors (again, just to illustrate
the ratio) as the stern would hit the frame of the flight deck shuttlepad:
(And if you were to take the shuttle down to the hangar just the way it landed, the angled-in bow of the shuttle would not get in touch with the frame opening of the flight deck and therefore work nicely with a diagonal shuttlepad lift.)
"The other thing is that in JTB and TIS we see the back wall behind the shuttle while in the hangar deck and it looks vertical, IMHO."
Most likely it is a vertical wall of the soundstage IRL, but one that's completely devoid of discernible features that would tell us that the producers intended it to be vertical.
But if we were looking at a vertical wall and a vertical lift shuttlepad and considering the height of the hangar bay, would that not place the starboard side of Spock's shuttle outside of the ship
given the unique architecture below the flight deck?
P.S. Does anybody know what the white text sign (?) on the port side of the flight deck says? (the one between the cargo container chutes or whatever these are).
P.P.S. Found this link with some unbelievably neat stuff and original VFX flight deck shots (including the text of the signs!):
It also - in a multiple sense - puts the flight deck in perspective.