Yes, go with the eyes. In fact, go all the way with the eyes and make them grafted undead beholder eyes! Building off of
Bronz Dragon's nasty,
disintegrate rays take care of the tunneling,
telekinesis rays let it ferry troops into its mouth, and
cure critical wounds rays turn the thing into a floating sickbay. For added fun, mount dozens of
vampiric touch eyestalks along the edges of the creature, so it can launch horrific broadsides of negative energy.
I'm thinking
disintegrate and
telekinesis stalks mounted at each end,
cure critical wounds stalks in the interior, and
vampiric touch stalks mounted every ten feet or so along the perimeter. That sounds like a lot (and it is, 200 or so per broadside) but their range is such that only 12 will bear on one target at a time, and even then the poor sap has to be standing right on the troop transport.
So what's to stop the PC's from targeting and destroying these eyes? The diversions. Use
Samnell's ideas for eyes, distributed all over the creature's body. If memory serves it's not immediately obvious where the beholder's rays are coming from. They could, of course, just fireball the entire general area.
The big problem is
finding that many beholder eyes; the number of
vampiric touch stalks can be scaled down as needed, though I'm fond of the idea of ghoulish flotillas sweeping across with negative energy broadsides like naval commanders of old. Maybe a separate creature, only twenty or thirty feet long, which serves as a ghoulish destroyer?
This is a link to the True Ghoul template:
http://home.gwi.net/~rdorman/frilond/rul/dm/ghoul.htm