Just got back from a 40 mile ride. To recap, the bike is running the Lloydz high-flow air cleaner that uses the stock cover, Indian Stage 2 cams, the stock unmodified Indian slip-on mufflers, and a Fuel Moto Stage 2 tune.
It runs great, no issues at all during my test ride. The bike is strong and smooth. I can't attest as to how it would be running using the Indian Stage 2 calibration that comes with the cams however.
Sound-wise, the tone is deep and sounds really good during acceleration. While cruising it is very quiet, which I'm happy about. As I say often on here, I'm primarily a longer distance rider. I do at least 1 very large multiweek trip each year. When I ride locally, it is rarely under 50-100 miles. While aftermarket pipes sound cool, they are utterly annoying (to me anyway) after a few days on the open road. At that point, I just want to relax and enjoy my tunes. The lopey cam idle is still there obviously, but not as pronounced as it was with the Vance and Hines Classic slip-ons. That was never a thing I cared about though, I don't get why people care about what the bike sounds like at a stand-still, I'm moving 99% of the time.

I guess if I were a bar hopper or something and I spent considerable time standing around talking about the bike instead of riding it, then it might be more important? Who knows on that one.
Anyway, as of now, I think I'm done modifying it. Fuel Moto did send me 2 tunes, so I'll try the other one as well for grins. I could actually stand a
slightly louder exhaust, and wouldn't even mind it so much, but I also don't believe that one exists on the market that would be appropriate short of the Indian Stage 1 pipes which are horribly over-priced. I put a set of S&S Grand Nationals on my Harley over the weekend, and they sound fantastic with the baffles intact (they are easily removable on those, but I don't see me doing that). I wish they made those for the Chieftain, I'd buy a set right now. I guess I'm going to sell the Vance and Hines pipes with 400 miles on them on eBay.