heres my 2 cents. the guy a duncan may be an ass, i dont know but he is right. without airbox mods a slipon will only make it louder (adding the header and mid pipe wont help either) your raptor will only flow as much air as the the most restricted part will allow. in this case the air box. the 660 air box is very restrictive and will have to be modified if you want any performance gain. i suggest something like this https://www.ebay.com/itm/MoFlow-Airb...onmQ:rk:7:pf:0
i ordered the outers fabric and made my own ( i am way to cheap to spend that kind of money on something i was able to make in an hour)and added a k&n. it does a pretty good job of shedding splashes but would not hold up to deep water.
that being said i suspect your problem is in the rebuild of your carbs. i suspect that if you had the old muffler you would find it runs the same. adding that slip on would not cause jetting issues bad enough to create your problem
i could not even begin to count the number of carbs i have rebuilt and tuned but it is a lot and 2 years ago a picked up a really nice 660 for my wife and after one or two rides i figured out why i got it cheap, the carbs were leaking and it was boggy in the middle. i thought no problem i will rebuild the carbs. well 2 days later i got it done but they were the hardest carbs i have ever done. the main problem i found in hers and what i suspect happened with yours is the is the guts from the right carb ended up in the left carb and vice versa. as i was rebuilding them i started to do the same, it is really easy because as you work on them the left carb is on the right side because they are upside down. tuning, balancing, and setting the floats was also a real bummer. did you use a manual or just take them apart and put them back together. each carb is jetted slightly differently and handle different stages of throttle. ( this is why so many people changed to a single carb back when these were the hot ticket). i am not judging your skill just saying it is really easy to do. also double check the carbs in the boots they are a little tricky sometimes as well.
as far as the jetting goes i know the plug is no fun to get to but at least you dont have to pull the tank like i do on the yfz's. the plug is critical to getting the jetting. there is no magic number because each bike is different. the amount of vacuum the engine creates plays a roll in how much fuel flows through a jet. the tighter the engine the more vacuum it creates, the more fuel is pulled through the jet. so a 155 may be different in my bike as compared to yours so checking the plug is the only way to get it perfect. the header and mid pipe wont make that much difference so if you do the air box i would start with the duncan numbers and move from there. if you dont do the air box i would be surprised if you need to rejet at all.
i installed air mix screws like these https://www.ebay.com/itm/Raptor-660-...l3J:rk:10:pf:0
i think mine were mod quad but i am not sure. i found them critical for getting the tune exactly right. i have those or the flex jet screws on all 6 i my bikes and i will adjust them throughout the day as the air temp changes, especially when i am at the beach. if you dont have one i really like the clymer manual it was very helpful getting those carbs perfect.
i have only worked on mine and that is what i found. hopefully digger will be on in the next day or so, he really knows these machines and may have solved this issue for someone else. again i am not trying to knock your skills but that is where i would start if you brought it to me with the information given. let me know if you need anything else