With the XCT hard lowers, less is usually more. Start with them open about 1/4 inch and work it out from there. Stock, running hot, and now running cooler makes no difference with them, you have to get the air flow right. Many times I'll shut mine completely when it is real hot.
Too many things to factor in, and heat tolerance for the rider certainly is one, so it is hard to figure out over the internet if you have a real problem or just don't have the tolerance that some do.
Sounds like you may want to remove the lowers in warm weather until you can get it looked at.
As for the stalls and hiccups, is this new? Seems like even the better of the tuners want to pawn "the nature of a V-twin" on some things. Not saying they are without their qualities, but some things I won't tolerate and my bike doesn't do. If it did it would be fixed or gone, so you have to decide from there.
Some people go their whole life wondering if they made a difference, Marines don't have that problem.~ Ronald Reagan
2012 XCT, AFR+ Gen 4, Lloydz air filter. I don't equate noise with power.
I ride with the Force.