No reason why you couldn't put a manual gearbox on, even if it had an automatic in the donor car.
(My mate has got a V8 engine in his Landrover that came from an automatic Range Rover, and just swapped the box over)
The main considerations are then finding a decent manual VR6 gearbox. And how much extra time and money it will take.
You'd probably take the gearbox off during the conversion process anyway, so you could swap it at that point.
Oh the other thing is what you do about the clutch, (someone correct me if I'm wrong) Mk2's are cable clutch and the VR6 is hydraulic, so you need to work out how you're going to accommodate that, ie do you change the pedal box for a Mk3 hydraulic item ?