2004 Vulkan Classic 1600 issues

[Mystussnake]

Hey Everyone, Thanks upfront for any help that is provided. I recently (2 m onths) purchased a used 2004 Vulkan Classic 1600 with 27,000 miles on it. Since that time I have put 2000 miles on it (as of yesterday) around 1200 miles it started "acting up" on me. I would like to premise that the gentleman that owned it before me took real good care of it. I spoke to the shop where he mentioned that he had it serviced and they confirmed this. I have it scheduled to go into that shop in 2 weeks (they are back up that far) but I wanted to look at a few things before taking it in. What is occurring is after about 20 minutes or so of riding the bike starts to "stutter" almost as if it is not getting enough gas. It doesn't seem to do this much in high RPMs although occasionally it still does when reved. It does this most at cruising speeds between 40-60 although it does it occasionally at other speeds as well. I checked the spark plugs and although they were "ok" I changed them out for new ones. I also checked the air filter which was somewhat dirty and clogged near the top of the filter. The rest of the filter was clean. It is a reusable K& N filter so I bought a kit, washed it, recharged it and put it back in. My bike ran better but the issue did not go away. It seemed to prolong how long it took to start "acting up" Instead of 15-20 minutes of riding it now takes about 20- 30 minutes before it starts acting up, but that may just be anecdotal. It has never had issues immediately (within the first 10 min). I also checked the battery, connections and all. I have a volt meter that read 12.6 and my bike has never had issues starting. The connections were very clean and the battery is a fairly new Xtreme AGM battery. It appear that the vent covers were slightly bulging but when I took them off nothing appeared to be damaged and the vent covers went right back on. There was a very small amount of leakage (white line of crystalized sulfate) from one of the vent caps but nothing that looked to be a real issue. I looked at the throttle body and although it has a small amount of carbon build up near the valves nothing appears to be too dirty or damaged. I looked over as much as the bike that a could and didn't see any glaring issues but I am extremely new to bikes and automobile mechanics. Im a quick study but only in the basic stages of understanding my bike. I have a power commander 3 that appears to be functioning correctly but how would I know. Any suggestions anyone? Your help is much appreciated.