I suggest giving the carbs a good cleaning per the carb guide.
http://www.amckayltd.com/carbguide.pdf
It never hurts, only helps. The old gas will varnish the insides. After a bid of running these pieces break up and find their way into the little ports, clogging them.
If you left gas in the tank, clean that out as well. Ya, you might waste 10 bucks with new gas, but it's worth it.
Always listen to your plugs. Do they read lean? Rich? Were they gapped correctly? What happened when the plugs fouled? Did you change anything? What is the mix screw set at? Are the carbs synched? Idle screw setting? Lots of stuff to check. One adjustment missed can cause a problem.
With cut pipes and cone or pod filters, the jets, as you probably know, need to be changed. Were the jets that were drilled stock then drilled? I would just buy new jets. I really got tired of screwing around and bought several new jets, read the carb guide front to back then sideways, and did a little "trial and error" testing. Runs great now.
If it sat since Sept I really suggest a good clean and adjust. Oil changed, cam tensioner, valves, timing, carb cleaning. Even if it was only run a few miles last season, change and adjust.
These are some suggestions that need NOT be over looked. The XS will complain if it is not maintained.
Also, put some info about your bike in you "signature". It helps others help you. Read the carb guide, believe me, eveyone will tell you this.