Thanks for the feedback! The difficulty in finding the problem launched me into getting the DRBII emulator.

Steps I have taken
Verified that the electric lock pall has been removed by the previous owner (unfortunately he did not document that removal). DRBIII showed lock works
Replaced the bad battery which was only one years old. DRBII shows good voltage
Bought and replaced the bad divider brackets (sensors change state in DRBIII when it is moved)
Thought I cycled the top manually to sync the top

DRBIIII feature missing

One thing missing in DRBIII emulator (I think) is activating the "closed trunk lid sensor" by itself. It reports the status in the opening and closing report, but you just can't closes the lid and see it activate.
Next Step
I am first going back to syncing the top with the help of my wife.
My most recent efforts (solo) have been using the DRBIII emulator.
My understanding of the DRBIII emulator is gathered from documents, forum posts and fiddling with it in the last several weeks. I don't have an expert (yet) to show me the quirks, but I am picking up on it's capabilities.
In the system mode, it states what the present condition of each of the convertible sensors in the open mode and the close mode. (including the header and top switches). It also gives the state of all the sensors when there was last a "failure" in opening and closing.

All the convertible top sensors said "Pass" according to the DRBIII emulator, except the "trunk lid closed" which was a "Fail". This is why I was gravitating to it.

In addition, I operated all the actuators (windows, solenoids etc.) with DRBIII emulator and they all seem to function correctly. I have been focusing on understanding the DRB III results to give me the magic answer. So now, with help (after syncing again), I will start with the button pushing and focusing on the beeping sequence and DRB III status in parallel.

Another forum post mentioned that if a "top operation" did not complete that the "trunk lid close sensor" may not set. That is why I am now trying to use two people in the manual movement effort.

For sure I am not an expert in DRBIII, but I see the sensor values change as I try to change position of the roof. I was hoping that the DRBIII emulator would add clarity to this debugging process (which is very murky).

I will have more information after I get a helper during the debugging process. Moving the roof and watching the emulator at the same time is difficult.

I will be able to see the sensors in real time.

Fingers crossed