You can get a $50 to $60 induction tack, to figure out where your idle is set. You can google Roadstar idle and JD, or search the forum here in the blue banner above and see if you can find the vid, and or a post with the vid, for a comparison. It's difficult comparing the short pipes, to the longer ones just by sound. There is a noticeable difference between any type of dual, and a 2 into 1, as far as sound goes also. The 2 into 1, will always sound smoother. An induction tach, like the EZtach is the best way to be sure.
Do you know what jetting is in the carb
? Clip position on the needle? What's under the clip? Always nice to know those things, especially because people can get so far off the beaten path when rejetting a carb.
JD knows more about this then me when it comes to issues with short pipes, but if you have a slight leak at the manifold to head flanges, I would think it could cause some problems at idle, especially if the idle is set to low. The lope in the motor, would exacerbate the the weird idle, by messing with the fuel air ratio at idle when the vacuum behind the throttle plate is high and makes any leaks that may be there, a problem. Just a thought.
Make sure the exhaust gaskets are sealing properly. The Yamaha OEM's, are the best. The torque needs to be revisited several times over a week or so, on a cold motor, after the hot and cold cycle settles the gaskets/pipes.
Short pipes come with inherent problems, but if the idle and jetting are correct, there are no vacuum leaks or exhaust gasket leaks, and the coil wires aren't shorting against something, I wouldn't think the idle would step in and out like that.
I can get a change in idle on mine similar, when the temps are down and on a cold start. It is just at the start, after pushing the enricher in about halfway. The bike will have a slightly sloppy sound, then it sounds like both cylinders start firing properly and it smooths right out. Beyond that, I never get anything close to the weird thing you have going.