Hi TH,
There is a seal that runs under the narrow panel that fixes the back of the top to the drain rail. However, i would expect a leak in this area would be caused by the channel filling from blocked drains and the leak to appear in the back of the cabin where the top is stored in its down position.
You indicate finding water in the 2 rear-most low point on opposite sides of the boot. However, was the water found after a rain when you Healey was Parked of only after your car was Driven in the rain? Additionally, since water is being collected in 2 locations, is there any indication that we are dealing with 2 separate leaks or a single leak that is flowing to these 2 locations.
If the water only collects when the car is driven, the gas tank mount and seal could be leaking and water forcibly entering on both sides. Also, since the lights and reflectors are mounted above both areas, 2 separate but similar component faults could be allowing water to penetrate the lighting fixtures. Since the 1-piece rear shroud raps over the side boot wall panels and secures and sealed to the floor, I would not expect there would be even driving water penetration in these junctions unless you have 2 separate loose or missing outer fender-mounting bolts.
Again, it is important to note if the car is parked or driven when the rain water penetrates and if we are talking one or two penetrations to determine the dynamics of the issue.
Good luck,
Ray(64BJ8P1)