This is going to sound silly, but just happened to me. Just a couple of months ago, I was running into a hard starting issue too. I was letting the fuel pump cycle twice, and all sorts of things. Bike ran great but just took a while to get it to start. Unusual, because it always normally would start at the slightest flick. Nothing I tried helped and towards the end of the season it kept getting worse.
Two weeks ago, I got my arm twisted to do a Toys for Tots run and it wouldn't turn over at all. I had lights, but the starter turned over once, then nothing. I thought it was a circuit breaker or something? I took off the seat and was shocked. The negative bolt was very loose and the terminal was pretty well melted. Obviously, it had been loose for a while and arching.
I grabbed a 10MM wrench and tightened it up, and boom, it started immediately again. Naturally, I have to replace the battery, but seems this was the problem all along. I just can't figure why it never stuttered after it started like this?
I'd give that a check as this sounds real similar.