For the record I'm hoping that you are using a fairly lowish resolution so that the art style is consistent with the rest of the art. But yeah that doesn't look too great in its current glitchy state.
Fox did make an autoshading script that works in-game. Hendricks made a port of it to mapster script at one point but but was glitchy and several surfaces were unaffected. Nothing's really happened since then. A real shame since I'd make extensive use of such a script. In the mean time if there's not much coded behaviour happening in that section of the map, you could start it up in-game with the script running, then do a "dndebug" to output the map with the shading applied.
I've used Hendrick's sector mirroring script to do the underside of the saucer section of that Federation ship. So if he does decide to continue working on scripts I'd want him to know that they're being put to good use as opposed to sitting on a hard drive collecting dust