You may be having an issue with the stock O2 sensor making the Spyder run leaner in the hot temps than it should be. I know of several other people who are having this problem with the heat we are currently seeing, and my Spyder has done the same thing. FYI, it is not only Spyders having these issues with heat right now as some of my Harley and crotch rocket friends have been talking about it as well. I have been considering getting the O2 sensor mod from Evoluzione as that is supposed to richen things up some, and seemed to be the cure for PCBeachBum's Spyder.
Spyders run somewhat lean from the factory. When you put the Two Brothers pipe on for more air flow, the ECU was able to compensate for that change. Once you added the K&N Filter that was more than the standard compensation can handle, and your Spyder should have been running very lean. As you found out, it requires a fuel management system like the Juice Box in order to push enough fuel to rectify this problem. Once you get it dialed in properly, your Spyder should continue to run fine with the changes you have made with the air flow.
For those that are running stock, or just have an aftermarket pipe, the ECU is supposed to be able to compensate but it appears that when things get really hot the O2 sensor does not send the proper signals and we lean out even more. :dontknow: