that was DEFINATELY your issue. I've not seen many setups put an external gate off the hole for the internal gate's flapper. I suppose there is not a way or room to mount the gate coming right BEFORE the flange that the turbo bolts to and after the runners are collected? Eh, if it works now, who cares. HAHA, you bike makes more HP than my CAR. Not for much longer though rookie.
EDIT: That pipe in the second to last pic, is it still made the same way as we see it? It should probable be welded from the inside as well to melt down the lip of that pipe joining the flange, then ground down smooth. That lip will cause a lot of turbulance which you probably won't notice any side effects from, but to be RIGHT, which I know how you do your things (The right way), it should prob be done in your 'spare' time.