I've got 80k miles on my swap, using a 2nd gen ATS manifold. Its tight to the AC box but I haven't had any problems with it. For the first 70k I had an S300G on it and left the stock heat shield on the AC box in place.
In the last 10k I've upgraded to an ED 62/68 and had some serious wastegate issues which caused my EGTs to run a sustained 1100-1200 for over 1000 miles while towing. After I got the turbo back off I noticed that the plastic AC box had melted a little, nothing serious but it had melted. (I took the heat shield off because it was torn when I installed the ED turbo)
I'm sure this melting was due to the seriously high underhood temps from the wastegate/turbo issues. I say run the 2nd gen manifold and don't worry about it.