http://www.littlejuniata.org/flow-rates-on-the-j/
not sure what you mean by rapids. Closest thing is near tyrone milling.
Flies: its summer. Midges are the most abundant at daybreak or in the evenings. Crane flies in certain sections (for example upstream of pemberton) are intense. However, they don't fish well unless you land the fly almost right against a rock. I've seen some caddis, but they are waning. You could get a good amount of cahills.
Tricos in places.
fishing underneath with caddis pupae (sz18) or larvae (sz 16 and 18) and wet ants is your best bet
Consider joining the LJRA
http://www.littlejuniata.org
https://www.facebook.com/pages/Little-Juniata-river-Association/328874627907