Yes, the wagon will fit the ute, but finding a manual wagon will be harder than a manual ute I reckon!

VT-VY V6 manual ute or wagon are pretty much the same, except at some point in VT they changed the drive yoke on the front of the diff from a UJ yoke to a "donut" yoke - often called a "3 bolt" flange.

What's wrong with the tailshaft? Is it one of the later ones, like the Fords, where the uni joints are pressed in & staked, and you want to rebuild it?
Considering the rarity of the combo, if you can't find one easily, it may be worth spending the $$ to rebuild it professionally.

However, I have found one on eBay, 2nd hand: https://www.ebay.com.au/itm/231954326725
They send stuff all over the place by courier, so it doesn't matter if you're nowhere near there.

I had this mob do me a brand new FG tailshaft - with traditional uni joints that can be changed. All new parts, balanced etc for $450.
It may be worth asking them if they can rebuild the 2nd hand one for you before shipping it?

Here's an ad for a new one they do, so you can see what they offer as a new shaft: https://www.ebay.com.au/itm/332467938465