I think a mk3 Golf TDI box can fit but I'm not 100%. I remember looking at it as an option for a boosted 1.4 Polo.
It does not.
You have an 085 gearbox in the Polo, the Golf3 TDI is 02A - cable-change.
The key foible of the 085 in my experience is that the mainshaft bearing pressed into the bellhousing gives up and then the shaft gets on down and has a boogie in the casing.
The bearing that goes is an LT van rear wheel bearing, the cost-cutting b*stards.
You need to find another 085 gearbox, it's OK they were fitted to pretty much all the common Polo 6Ns, but it must be a hatch, not a saloon, or a van.
Those have 020 gearboxes fitted to them (go figure).
Fascinatingly the hatch 1.9D NA had an 085 gearbox fitted, but with a different bellhousing and without one of the lugs on the petrol variant.
Most scrapyards should have a couple of these Polos lying about 1.0-1.4 - they're all pretty much the same.. The one down the road from here sells the gearboxes at £40 a go.