So do you get the 30FF fault if you go back to stock boost levels? If it is totally fine with the JB removed, then getting any kind of warranty repair is pretty slim.
When I see a 30FF fault on stock cars, it's usually one of the EPDW's (wategate vacuum control valve) leaking or a wastegate mechanism binding/jamming. Or a broken or damaged vacuum hose. I've personally never seen a factory intercooler or bypass valve leak. If somebody left something loose, that's a different story.