I just got thru doing what your experiencing! I have a 95 650 savage, put on newJardine Muffler and you MUST RE-JET! Not hard to do just look in the treads here and they tell you exactly how to do it. This is where I got most of my info.
First things first, when you put on new muffler did you get new seal for it? You must do this first and then add some Hi-Temp Silicone around it to make sure you don't have any exhaust leaks and do same at Head Gasket! put in New one. After you do Carb Kit you must remove cap from adjustment screw and turn all the way in and then turn out about 2 1/2 turns or more, use this as a start as I had to fiddle with mine to get right. I carried a small screw driver with me for a while and would have to keep adj every so often to get it where it didn't POP. I get one once in a while but I can live with that! Not like B4!!!! I got my carb kit off Ebay but there is one on here that people rave about. I paid like 25$ for mine and it worked good. I did't replace any washers as everyone speaks of, maybe guy B4 me did done know but really don't think so as he had stock jets in carb.
To re-jet carb is NOT hard to do as long as you take your time and read the threads on how to do it. Hope this helps. And with the Jardine Muffler! What a difference and sound! Just Like one of the BIG BOYS now! Good Luck