would strongly advise against getting a second hand gearbox as it is likely to have the same weakness, also they are hard to find due to failures.
As the 1999 year cars are now out of warranty, I would not get a new gearbox as they are very expensive, and require a surcharge if the old gearbox can't be returned with intact casing.
Best option is to get the gearbox reconditioned at a gearbox specialist - not a VW dealer (which will be about 50% more expensive).
The main problem with repair is getting a new gearbox casing, it is possible that the old one can be welded depending on where the hole is.
The differential can be fitted to the final drive gear using a repair kit. The remaining rivets have to be drilled out and replaced with bolts and nuts using washer plates. Repair kit part number is 02K 498 088 for DUU, DUS, DUW, DUV, ERT gearboxes or 02A 498 088A for other 5 speed gearboxes.
Usually some of the gears are damaged by the loose rivet(s) and all can be damaged if ran for a while after the oil has leaked out.
The gearbox specialist I got mine repaired at said it was a common problem with these gearboxes, and that earlier year models had rivets made of a harder material, on later models the rivets are a larger size.