I would be less concerned about the heat (you will need forced air cooling if you're really pulling 3 kw, even intermittently), but rather the voltage drop under load, and its effect on the welder.
Right now this appears to be the best deal on ebay:
http://www.ebay.com/itm/Stancor-GIS-1000-1KVA-Isolation-Transformer-Works-/290611107263The 1 kva
isolation transformer at toroid.com is $160+ shipping, but its probably going to have a lower impedance than that Stancor transformer.
I don't think the 1 kva "auto transformer" which weighs only 7 pounds, is going to do you much good, and its still 110$ plus shipping.
If you do buy a toroidal auto transformer, note that you could connect it in parallel with your generator because you'll be able to add extra turns to cut the circulating current if needed.
However without knowing the resistance of your generator and said toroidal transformer, there's no telling if that's going to do much to load down the other half of the generator.
So what I would do is measure the electrical resistance of your generator (use a 1 amp current source and a volt meter) and call up toroid and ask them what the resistance of that auto transformer is, both the 1 kva isolation transformer and the 1 kva "auto transformer"
They may not know, nor want to tell you, but they might tell you what the wire gauge is which is just as useful.
FYI: IF that stancor transformer is wound with 76 turns of 12 awg wire for a 1.2T excition, it should have a resistance of 170-200 milliohms, which would be a 4-4.5 volt voltage drop for both primary and secondary under a 25 amp load. However, i have no idea what they wound it with, all i know is the frame size, the fact that it weighs 31 pounds, from there i can work backwards and get a stack thickness of 100-110mm, which means it should have been wound with 10 awg wire but I really doubt they invested that much copper in it.
if you were to pull 25 amps from it connected as an auto transformer you would be looking at a voltage drop of 4-5 volts or 4%; again assuming its wound with 12 awg wire and runs at 1.2T