You installed a BNR stage 3? What are you running for boost control? The factory boost control, or are you running a 3 port? I don't see it in your sig.
Also with a new turbo, running an OTS map is not advisable.
It seems like this has had views, but no one has chimed in, so let me say thanks. Ive gathered everything I need to do it using this method (except I was going to vacuum the chem out, the pump is a great idea), it was nice to see someone's had good results.
Focus on the same areas as you would have in the speed 3, smoking turbo at idle, vvt rattle on start up, vibrations from clutch pedal (rod damage). If you could get in there and check compression, might be a good idea. If it's taken to a shop have them check the rear dif mounts, and the front...
I hope you're also planning a set of fuel pump internals if you're running a DP.
28 highway is to be expected, especially if you were keeping it out of boost, stage one improved my mpg, Stage 2 did not, lol