Excellent team rey.
The only change I recommend is defensive CM Wish Jirachi over your current one. Not only do you maintain an almost 100% way of defeating stall, but you also gain another Wish user which would make your team even more annoying to play and beat. Psychic would remedy the Machamp situation as well, and also Breloom to an extent. The SD Infernape weakness will forever be unsolved however because of how slow your team is and how vulnerable it is to priority, so again like you said make sure you play Flygon extremely carefully or else you'll definitely be swept by like Lucario + Infernape teams.
Other than that, this is an excellent post-Latias and Salamence team. Congrats on the success.