Look in the tank. When the engine is running is there fuel spraying from any of the hose connections? The only fuel moving around should be a stream from the return line. Loose connections can leak enough fuel to starve the engine.
New fuel filter is NAPA 3032. Don't use the hose that comes with it, it's not rated for submersion in ethanol fuel. If the hose on the old filter isn't too hard or cracked you can reuse it. Otherwise, get some 5/16" rated for submersion. I'm sure someone with a better memory will chime in with the SAE rating.
You might also want to get a bottle of Techron fuel system cleaner. Put a couple gallons of fuel in the tank(non-ethanol if you can find it) and about 4 ounces of the Techron. Let the engine idle for a couple minutes to mix it and get it down to the injectors. Let it sit for a couple hours and start up the engine and let it idle, rolling on the throttle occasionally. Once the bike is roadworthy, take it out for a ride, keeping the rpm at least 4000. If the bike has been sitting, the injectors will have a lot of crap i them, and unless you send them out to be cleaned it can take a while to get them loosened up.