Regarding standard manifold/downpipes, I would have thought you may get some decent horses from a flowed s/steel manifold together with a s/steel exhaust, cone filter and a chip.....
I doubt it...I built a 2.9 12v VR6 that is now in my mates Mk3, it makes 228 BHP, 208 lb-ft, and revs to 7500 all day...and uses standard cast manifolds and downpipes, match ported.
The standard VW stuff isn't restrictive...so don't assume you will get a gain...because I very much doubt you will.
Much of the aftermarket SS 6 branch stuff is crap quality and will end up cracking anyway.
If it were me, I'd see if an OEM mix and match solution can be found.