Well its hard to say based on that but the only thing that sounds %100 mechanical is the puff of smoke through the vents. Your stock electronic boost controller is probably still fine so i wouldnt replace that just yet. Its very possible a few of your other issues are related to the mods and the tune designed for a lower altitude.
I wouldnt want you to drive the car if there is a mechanical issue and im not real close to commerce city.
Pm me and maybe we can work something out.