Let's see if we can clean that up a bit...
My take on the "Refit"...
The original “Big E” was designed as a series of circles and cylinders; I would want to go with that theme as much as possible. So as the refit goes I would leave the exterior as is, with the exception of the engine nacelles and their support pylons. Over all beam and Length and Draft as per TOS/TMP. No uber ships (No bloody C, D, or E as Scotty would say
One of the great losses from TOS is the turbine effect of the engine nose caps. So I would choose the cylindrical engines, same length, with an over all design along the lines of those on NX01. The engine support pylons would be similar to originals but, with a slightly larger chord and small fairings at the root and engine.
Color to be either gull gray or left in bare metal finish... (6 of 1, half dozen of another)
Runabouts from DS9, the rest are scrap, except for Work Bees…maybe
Problem: a Danube class runabout is rather large. The cockpit section alone is the size of a Class F shuttlecraft (like the Galileo). I doubt you'd be able to easily fit a runabout in the hangar bay.
There are many good possibilities already designed from other ST films and TV shows, the bridge for example would be from ST V, with the officers ward/briefing room based on the design from the Undiscovered Country.
In the engine room I would just up date the TOS design (detail it out some) as I love the EMM portion of the set as well as the functional over all look and depth it adds. (All of the cute 50’s plastic walls and engine core tubes are definitely gone.)
The railroad track photorp launchers would be replaced with something that more closely resembles an artillery piece. (This is the 23rd century)
The Sickbay complex would be closely designed like those from Undiscovered Country.
Transporter room from ST: NG as are most of the halls, turbo lifts and crew quarters… (No multi man bunk rooms.) two crewmen to a room…only. Senior Officers/Department Chiefs and VIPs get singles. (No families!!!)
Put them all in the incinerator and back to the TOS stile…the only exception being the neat “Field Jackets” of TMP. Space suits suffer the same fate, keeping only the suits from WOK.
Weapons et all…
No hand vacuums, hokey push pin communicators, wrist watches, etc. TOS communicators, Phaser I’s, and Undiscovered Country stile Phaser IIs, Phaser Rifles from ST: Voyager.
Note on crew duties: One man one job… the helmsman is the helmsman not the communications officer/weapons officer/navigator/helmsman/add nausium... NO, I repeat, NO beaming around/to and from the ship’s bridge or any other place on the ship for that matter...LOL
And what happens when the helmsman gets hurt? Or the communications officer goes balmy and shorts out the system? Or half the crew is down with the Rigellian flu? Knowing more than one job is a simple fact of reality on a starship on a deep space mission, where you can't just send back to base for a replacement.