Welcome to the site. I guess reflecting back now I am not sure what to think of the ported heads actually. Honestly I did them way too soon. I did not have other things done first to get good data. I had long tube headers, x-pipe, catback, CAI, throttle body, a not so great tune, 3.73 gears, driveshaft, LCAs and shocks/struts; but only had one day at the track with 4 runs on the car at that point. So I had the intake and exhaust mods for the heads but didn't have a good tune worked out, was having O2 sensor issues with the long tubes and traction issues. I should have had all that worked before doing the heads. They definitely flow more air, there is no question about that. I still wonder if cams would have unlocked the heads potential more.
I can't recall what MPT set my shift points at any more. But I have a Circle D torque converter too.
I would guess that a ported lower will give more gains than the upper because of the injector bumps in the lower.