What about prices in your country? Are they higher? If I'm correct you're from Canada.
It's difficult to put a price on that type of vehicle as each one is privately built by an individual. There are a lot of variables but each one pretty well has to start with a vehicle that is currently owned or specifically purchased for that purpose. Generally in my area such a vehicle, with a bad auto transmission, will sell for $1000 to $1500.
All of the required Tdi parts have to be sourced, either thru junk yards or purchased from someone that specializes in that sort of thing. In my case the "kit" parts were sourced thru Dutch Auto Parts in the Netherlands. I received a proper Tdi transmission (not readily available in N/A), subframe, clutch pedal, smf and clutch and maybe other bits and pieces that I've forgotten about. Don't quote me but I seem to recall that package cost app. 1350 euro.
Some individuals are quite capable of doing all of the work themselves and others will get a shop to do the work, which of course will mean an added expense.
The ECU will have to be tweaked to recognize the manual transmission and that will again cost a few hundred dollars.
So as you can see the costs quickly add up.
Most people will opt to have the BSM deleted and if the vehicle is an unknown entity they will most probably have a proper timing belt replacement done as well. And if it's a high mileage vehicle, the suspension, brakes might also need refreshing. It keeps adding up.
Most of the vehicles will not have leather interiors and if that is important then you are off to the junk yard again looking for a suitable interior.
Now that you've gone this far you might decide that you also want new tires and maybe nice new rims.
You can see where we can easily spend as much money as what your vehicle sold for, but we don't have a proper factory built car, just an imitation. But we enjoy them.
I hope this answers your question.
ps I should also mention that I would very much prefer to pay $5500 up front to buy a wagon like yours than go thru all the bull**** to convert one.