should have clarified on the valvetrain noise, its started whenever i set my valves to factory specs, there were very tight. now they the just are so tappy i. i have heard other xs owners commenting on the noise.
You don't state your level of mechanical expertise, so I'll go over some of the basics here - feel free to ignore if I'm telling you stuff you already know.
Do you have stock pipes? If not and they are fairly open you will probably never get away from decel popping. If so then you're probably a bit lean or have some air leaks. You haven't replaced the stock air filter with something "freer flowing" without rejetting have you? That'll make things lean for sure.
On the valves - what clearances did you set them to? Are you sure you were on the correct TDC when you set them? On one TDC both valves will be shut, on the next TDC both valves will be slightly open (that's called overlap). If you check/set the valves at that TDC you will end up with <really> loose valves and it'll make a lot of noise.
If you set the clearances to spec, roll the crank 360 degrees to the next tdc and the clearances are tight you've chosen wisely. If not they'll be even looser and you have chosen poorly. Set them again.
Also - it's easy to mix up metric and SAE clearances - often the manuals spec in metric like .10 intake, .15 exhaust. That's in mm. Convert that to inches and it's .004" intake, .006" exhaust. Those are reasonable clearances for most bikes. .100" intake and .150" exhaust are not reasonable clearances and if you set to those you'll be very tappy indeed.
Does the bike have a manual cam chain tensioner or automatic? If manual make sure to adjust it. When checking valve clearances is a good time to do that.
Yup - with that setup you'll never fully get away from the decel pops/backfires.
What valve clearances did you set to? Also - is that a screw/locknut type adjustment? If so - has the screw pounded a divot in the top of the valve? If it has you won't be able to get a true clearance number with a feeler gauge as the gauge will "bridge the valley" so to speak.
Some aircooled bikes do make a fair amount of mechanical noise when set up right, but it shouldn't be excessive.
valves were pretty tight before. then the were set by feel by a mechanic. i then later set them as best i could using a gauge. after driving a few days a locknut fell off onto the top of the cylinder, removed the valve cover fixed it all up, then set them using a gauge, i set them using my owners manual to spec. i didn't know if wear made it so i ought to set them a little tighter or looser, or if its an oil issue. but i have heard from xs650 owners that the top end sounds like its going to explode but it just keeps on trucking.