I just completed the JMT southbound from Yosemite to Mt Whitney - 14 hiking days from July 4 - July 20 (2 layover dates). To the best of my knowledge, and from information gleaned, I was approximately the 10th person this season to complete the southbound journey.
So let me say this - Do Not Be Afraid. The trails are very passable, and getting better each day. I dare say that within a matter of days all snow will have dissapeared from the trails save the largest and highest snowfield (Muir Pass, Forester Pass).
Bugs, as everyone has said, are only a problem when you stop moving. I only encountered a few locations where bugs where a major issue - outside of Edison Lake, Rae Lakes, and one or two streams.
As per night-time bivy/tarp handling of bugs, try getting one of the cheap Army surplus style headnets - the ones that come close to your head. Wear that to bed while keeping your sleeping bag tight.
No specialized snow gear is required at this point, nor could even be used. The snow that is left never truly re-freezes overnight, and is slushy much of the day.
Stream crossings can be hazardous - although the water content in the area has peaked as of mid-July, there is still tons of it out there. Talk to other hikers on the trails, see what they have to say.