Good question, let's see:
I've found good fishing on the early flood at Joppa, but only for 30 minutes until I get the heck out of there.
Also, from a boat on the shoals out in front of the charter boats on the early flood.
The rockpile at the refuge has been an effective early flood spot for me.
Anything sticking out in the current at the mouth of the Ipswich has been explosive for me on the early flood.
Hampton between the end of the bridge on the MA side and the fishing terminal to the south, there is a little flat with a deep channel that the fish barrell up through on the flood. Also all the way out there at the rocks at the corner of the beach on the early flood. With a little skiff, the shoals in side Hampton are fabulous on the flood.
Salisbury between the mussel beds and the jetty as the tide rolls in has been good for me in the past, especially when there are herring in the river. You can tell because they come hide around your legs and won't go out into that current even when you kick your legs, they come right back in. Put on a good looking fly and >WHAM<
Cranes fishes well on the flood, but it not in line with PI-Kittery.
My observations are the same as yours, the fishing turns off as the tide turns incoming. Based on info from other locations I'm sure they go into high-gear to motor to the incoming tide stations upriver, or go greet bait that habitually enters the estuary with the flood.
We are probably finding them at their low tide station where they hold thru the bottom of the tide and I believe they just bolt up river as soon as the tide permits. It would be interesting to test that theory anyway.
When I fish the flats on the cape, the fish clearly hold in deep holes and channels thru the low and go into a mad scurry to get onto the flats as soon as the water level will allow them to get on. Most likely to pick up sand eels as they emerge when the tide washes over them.
I tried a little test last year at Browns. Wondering if Markey's was the only place with hand fed stripers, I saved a couple steamers and threw them off the Browns side during a hard incoming tide. Within 10 seconds the little cove was swarming with stripers eating my leftovers.