Our trip was in May with no flying bugs but may not be what you see. Still one of us picked up a tick at a campsite.
We paddled the whole length and recommend you start as far north as you can arrange. The river is faster, more wildlife/fewer people. We started from Pittsburg but most start from Canaan to save an early portage. The first day was the most fun paddle.

We did not appreciate portages. Move the kayaks a couple hundred yards, no problem right? Not so easy. First the water flow slows from 1 mph to nearly a stop in the reservoirs. Second some of the portage trails are steep (like hard to walk even without carrying any gear or kayak). All part of the experience but expect an hour river time lost per portage. Makes you appreciate leaving home anything you didn't need. Every ounce counts!

Enjoy your CT river trip!