@Alex - thanks for your kind words of encouragement and I'm glad you noticed the outboard grilles
On the nacelle I positioned the m/am components to correspond to the forward ventral gray piece as I've seen the idea of a swappable component on other layouts. The ventral red rectangle hatch behind the pylon I figure could be used to access large parts of the energiser in the nacelle.
The yellow and red hatch behind the bridge I guess could be for some type on in-flight refueling station. (Assuming an aviation model, the B-52, F-105, etc aircraft of the 1960's had their inflight refueling equipment in very close proximity to their cockpit.) When the TMP redesign/refit occurred it could be explained that the area was expanded to also include a personnel docking station as well since the fuel piping was already there
The yellow and red hatch on the port side ventral of the primary hull I'm thinking could be for loading/reloading the photon torpedoes or for refueling the torpedo antimatter tank. I think that when Kirk took command the Enterprise was removed of her lasers and other weaponry and refitted as an all phaser gun ship. After "Balance of Terror", a photon torpedo system was added to the primary hull but instead of running antimatter fuel piping to that location, a small fuel tank was located there instead. In TMP it could be explained that with the relocation of the torpedo launchers to the neck, the EVA room expanded or was returned to it's original location
Anyway, those are my current thoughts on those hatches
Oh as to the bottom hatches on the engineering hull in ST5 and 6, I'm tempted to ignore them since they weren't seen on screen as far as I can tell. I think also the TOS engineering bottom hatches weren't really visible as well but I was lucky to come up with parts that worked out with the shapes. Otherwise, I would've left the TOS hatches as generic markings for other equipment