I just swapped my motor out a week ago. I put a brand new 02 sensor in and did the ATF trick. Now when I turn my boost up to 9 lbs, after 5000 rpm my Air/Fuel meter goes into the red, which means I am running super lean. Are my secondaries screwed or do I just need more fuel?

 

Into the red ? At WOT ? And you are still running ? Amazing...
Red area is very lean, and is a condition your engine should see ONLY during braking. Not in cruising, NOT DURING WOT. You are obviously running too much boost, and/or your fuel is inadequate (at best... ). Please check above before next WOT...