I have had my fair share of axle/boot issues. It is not a fun job, especially if you are taking a part off to deal with a warranty issue. I would really recommend the Raxles or VW OEM part from the dealer for your axles.
I would pay $75 so many times to not have had the issues with other brands of axles. And no, I did not buy refurbs from Autozone... but they were not EMPI either. I actually can't remember the brand.
But, from what I have read from other folks on this board... Raxles or VW OEM is worth it for this particular part.
ECS rocks for everything else, though!
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As far as your question of what else to do while you're in there... I actually don't know what a clutch job on this car entails (still on my original on my '98 w/ 140k), but I would do a good review of your timing belt, water pump, and accessory belts.
I would imagine your PCV system could use some love while you are under there. They seem to start clogging up very quickly on 1.8ts - at least the earlier model years.