If the columns on the Column Tiles fail to reach your ceiling height, why not just copy the column model, invert it and stick it on top of the existing column. Should reach the ceiling height, right? Then just give the tile a standard open floor ceiling. Not the most elegant solution, but WAY better than nothing. You could always use, say, the model from the Transporter Tile, inverted, and placed on the ceiling to give the column something to rise into. (Minus emitters, I think)
And for the Transporter Tile, definitely an inverted version of the transporter, preferably with emitters, on the ceiling above the ground one would give a very nice portal effect, especially with some dirty great PHoD Rubbish VFX plastered in between.
As for the problem with the Fighting Pit - since it doesn't directly link up with corridors and such ANYWAY, I'm sure the great majority of us would still love to get our hands on this set with ceilings, even if the Fighting Pit just got left unceilinged. Unceilinged? Is there such a word? No. Maybe. Well, now there is.
A nice successor to the Beholder Caves; it'd be a shame if this work were to be for nothing.