I agree with this. To me, it shouldnt really matter what "Stage" the tune is and what mods you have. The tuner is going to tune the car for AFR's, boost, etc, etc. Hes going to see how your engine is behaving when he sees your log and make adjustments from there, regardless of what mods you have.
I have a JST custom E30 tune, and changed the intake to an ITG full intake, re-data logged the car, and Brian said there were no adjustments that needed to be made even after installing a new intake. Ronmcdon is right, I dont think any of it really matters, "Stage" wise. Then again, I could be completely wrong. Lol