Bro somethings very wrong I have your same 05 C6 w/A4 but have 3.90 gears & huge Z06 19x12 rear wheels w/345/30/19 pilot tires (they cause HP loss as well) other mods cat back bullets, Vara ram, throttle body spacer full dyno tunethat's it no headers!
I put down 360 rwhp 355 rwto on Dynojet, w/Headers I'll easily be at mid 380's!! maybe your stall converter if messing everything up?
& yes I was told the same we will/do get losses from running these bad ass gears, dyno operator showed me other C6 w/A4 trans and similar mods making about 10-16 more rwhp w/fact 3.15 or 2.73's
You obviously have a tune w/new gears on the Automatics it's impossible to drive w/tuning the rpm/rev limiter, but did you NOT go for the full perf tune as well??
What was your pre mod dyno at? IE..Bone stock dyno?
I say if you haven't had a full perf tune yet, and your running Long Tubes, you're missing 25-35 rwhp:huh: