I heard something on that, it was found in some crate in southern Utah, from a cbs employee's estate. after that no mention of what happened to it. someone else said that gene smashed it to pieces in a fit of anger or something. I just don't believe that one, but who knows? im sure all this stuff was stolen and is in some rich Japanese guy's secret museum in Tokyo.
No, that was an access hatch, I believe, which Spock used to make repairs in Metamorphosis. It opened and dropped down. Next to the hatch was a red reactor flush vent, as I recall the original AMT design plans. There were a series of vent-like strips along the starboard bottom but I can't recall any labeling for them. The nacelles that hung off the pylons were for warp and the impulse engines were across the top of the aft hull and lit up during the original run of the show. I don't recall the bustards on the warp nacelles ever lit up in the original broadcast and don't believe that the AMT filming model had lighting there; only on the aft impulse engines.
Just for interests sake, the same design was copied for use in the executive shuttle, used in STVI, I think it was, and then those were engines again for the Sydney class in the Next Gen, which was a modification of the executive shuttle, scaled up.
Paragon made some great models of these two later designs.
There is one other trick I use sometimes, I put the sheet in ms paint edit, and then lasso cut and move all the parts into the smallest space, allowing for enough room for cutting, then I shrink the border so its really snug around all the parts. I then print, uncheck the box for sizing so the parts fit and if its really got a lot of border, I then go back and space the parts until it fits the print preview with as much of the parts filling the printed page as possible, I will even print on copy paper a BW test and again space the parts if there is too much border until im satisfied. the scale when compared to other models is off, but you get the largest model printed page. If that don't make no sense, [sometimes my explanations are long winded and hard to understand], tell me here and I will post an example.