The service manager did some investigating for me on both the manifold and the flash through his technical resources at BMW. Their response was disappointing, but not unexpected - no chance of a flash and the manifold should be OK. So, I'll likely go with the AA tune but not until next summer as I won't be putting enough driving time in during the winter for any software adapation.
One thing that I have noticed on cold starts (and maybe this will change as time goes on) is that the rough agressive sound of my PE during the first 45 seconds or so of warm up is now significantly softened, similar to what has happened to my PI sound.
'09 128i 6Sp Man Sport (263 18" wheels), Space Grey / Coral Red leather, BMW Perf Intake, Exhaust & Suspension, 3-Stage Manifold, AA Ver 2 tune, Carbon Filter & CDV Delete, Yoko S-Drives