That sucks big time! I'm surprised in a way that someone wanted to steal a stick truck (since most thieves can't drive a manual). But the wrecking yard may be your best bet on parts.
I think in my parts stash I have a pair of the column shrouds, but they're for an automatic column....
I believe when
@kennythewelder converted his '97 to floor shift, he made a filler piece for the column, for the hole where the automatic shifter goes, though, so it might not be too difficult to fabricate one.
If you haven't found the shrouds by the end of this coming week, PM me and I'll see what I have. I'd send them to you for shipping costs if you need them (and I'm remembering correctly that I have a pair!). Most trucks in our yards are theft recoveries and the columns are trashed, but every once in a while I find a decent one.....and I'm hoping to get a yard run in next week!