Typical excuse. Tuner screwed up big and wants to blame the bike. If you did those mods without tuning, and installed them by the book, engine would've needed tuning for optimum, safe AFR, since you increased intake and exhaust flow, but it still would've ran nicely.
Some tuners, man. They overconfidently bite more than they can chew and then create fantasy situations to shift the blame that is only theirs.
In no reality would those mods cause such issues if properly installed. It was the tuner being incompetent. Get your bike back before the shop ruins it with bad timing, and send it to a reputable tuner. They didn't need to touch timing AT ALL.