Do a search and post the question over on Planetisuzoo.com. There have been people going from auto to 5-speed, so I don't see why not. You would need pedal assembly, TCU, transmission and transfer case (T-case/transmission on the manuals are a combined unit. I'm guessing you are probably looking at about $3,000, so it may be worth just buying one with an auto to begin with.
Maybe a better way to go is to see if you can find someone on Planetisuzoo with an auto and wants to swap to a 5-speed, and just trade parts. I think all parts in question are compatible with any second gen Trooper or Vehicross.