I really dig the design, and the redesigns are progressing very nicely. Since you seem to be liking the input, here's another two cents...
-the side windows are a nice touch (and seem to invoke the look of the DS9 runabout to me) but are superfluous I suppose; and...
-especially in the TOS era, the engine area of a small ship should take up internal space, so...
-eliminate the aft door and make that "door" the impulse engine, and move the side door to just behind the cockpit, i.e.., in front of the nacelle?
Easier, quicker access for the crew, perhaps doors on both sides of hull, and the feeling of a big engine at the back of the shuttle makes sense to me. Whether it's canon or not, I like to think that shuttles have some warp capabilities and the core will have to go somewhere...
Anyway, just a thought. But me likey Ewloe big time