UPDATE:
So its been a little while since my post and I finally got around to installing a walbro pump this last weekend. Looks like my problem might be solved!
Install was easy, only took 45 min-1 hour, then I reset my ecu and so far so good. Car pulls hard through every gear with no hesitation! (yet) I guess the stock pump couldn't keep up with stage 2 and it was making me run lean. I'll have to give the ecu a week or so to learn and see what happens before I'll know for sure though. But overall a big improvement.