I've got a 2nd gen header on my CR... same turbo location as a 2nd gen manifold. the 2nd gen setup sounds a million times better.
a 2nd gen downpipe fits great... But, if you're using a 3rd gen turbine housing, you'll need to get a 3rd gen v-band flange that will fit over a 4" pipe. you can cut off the HX40 flange or just leave it on there. slide the 3rd gen flange over the pipe, tack it once you get everything in place, and pull the pipe out and final weld it. I'm using an HX40 flanged turbine housing.
I'm using a -4 AN feed line and fittings. I just cut the factory drain tube in half and used oil rated hose and some hose clamps to bridge the gap.
a 4" dia 45* elbow with an AFE filter is my intake setup. I've got the air temp sensor just hanging in the inner fender. works fine
for the cold pipe, I'm using a 2nd gen turbo, so I got a 90* 3" outlet v-band pipe from Cummins. call Jeff (snedge), he might still have the part number from my order) and I used a 2nd gen boot and cold pipe... cut off a few inches of the 3rd gen cold pipe and butt welded it to the 2nd gen pipe. works good.
would obviously be a different story for a 3rd gen compressor outlet