If you stored the bike for the winter with gas in the tank, and didn't treat that gas with stabilizer and/or run all the fuel out of the injectors and fuel rail, there's a good chance that you have one or two partially fouled or sticking injectors. The same principle would apply to carb bikes, btw. Fuel sitting in the injectors, or jets in a carb, evaporates over time and leaves a varnish like material. Easiest first action to take would be to pour some injector cleaner into the fuel (don't go nuts, use the amount specified per gallon on the container, not the entire can) and ride it at low speeds where it seems to run OK. If it's a little varnish buildup, the concentrated cleaner should either clear it completely or at least clear it enough to verify that was the problem by the time you use up that tank of fuel. If it helps but still doesn't completely correct the problem, it's fairly easy to remove the injectors and have them bench cleaned. Even the typical Harley dealership should be able to handle it.
One reason it might run OK cold and progressively worse as it warms up could be that the injectors are sticking and leaking extra fuel into the intake. Extra fuel is OK when the engine is cold, and in fact is required for starting and decent warmup. Once the engine gets warmed up, however, excess fuel will make the engine blubber and run like crap. If it runs way too rich, you may notice black smoke from the exhaust.
Jerry