Your bike will not be running 'rich' just because you've fitted end cans. If anything they are more likely to make it run lean! There is no need to modify the fuelling with your exhaust (obviously you can if you want to, but it's not necessary).

As those above have alluded to, you're not hearing/noticing anything that wasn't there already - it's just become more pronounced and noticeable because your exhaust is louder. The popping is just the AIS system doing the same job it was before.

Just block the AIS pipe as has already been mentioned, which is free!

Read this thread...

http://www.xt660.com/showthread.php?t=5544

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