Buggin,
Those hard clearish hoses run from the top of the supercharge, near the TB (2 black hook shaped rubber vac lines). They snake their way from there between the supercharger and intercooler and tie into another Y shaped black rubber vac line that ties into the passenger side EGR. The the other piece of clearish hose ties into the drivers side EGR.

If you need close up pics let me know and I will go snap a few.
You should have ported that baby while you were in there cleaning the gunk out of it.

Cheers,
KrzyFast