[ntsqd]

Something that I found with the Shelby-Spearco kit on my Rabbit 1.6l diesel was that moving the waste-gate's boost reference from the compressor scroll to the far end of the intake manifold yielded a more accurate and consistent boost level.
Under high load, high boost conditions (driving it HARD!) the waste gate actually was opening pre-maturely because of the excessive heat generated in the compressor. My boost gauge was ported to the far end of the intake and under those conditions boost was lower than when not leaning on the engine quite as hard. After the re-routing of the hose I gained 1-1.5 psi (up to 7 psi from 5.5-6 psi) which wasn't hugely significant, but the power delivery consistency made the engine a little easier to drive.

If you're going to be after-cooled then just moving the ref port to downstream of the after-cooler would be good enough. In the second iteration of my VW turbo-diesel I plan on after-cooling and the waste-gate reference hose will be plumbed to the intake manifold plenum because it is close & easy.