2002 SAAB 9-3 repair Question Viggen power hesitation

Engine Performance problem
2002 Saab 9-3 repair Question 4 cyl Front Wheel Drive Manual 80K miles

After getting some slight engine upgrades (downpipe and intercooler), my Viggen was faster than ever for a couple of months. But now it hesitates when you step on the gas. Sometimes slightly, and sometimes so much that it "revs" like it's not quite in gear. I've taken it in to the shop a couple times, they find no codes and no bad parts. They suspected the clutch. The behavior is similar but not a perfect match for a slipping clutch because it can happen when you step on the gas and it's already in gear. It feels more like air being restricted. Anyone ever heard of this? The shop is stumped, and they're a good shop.