Was able to sort out the window reset as well as the convertible top reset.
All is good with the world.

 

AFAIK, just keep retrying the procedure.
I usually did it 2-3 times on each window.
If it’s not taking, and you do disconnect the battery again, touch the cables together to do a hard reset.

 

Yes sir. I raised the top and started over.
Driver window. Passenger window. Top up - hold 60s. Top down - held 60s.
What I missed as letting go of the window switch then hold up/down again for 2s.
And that click is more of a mechanical noise, in the door.

When things aren't reset correctly, to make something useful and searchable out of this post:
Not only does lowering the top do the pause thing after unlatching and lifting a few inches.
BUT, also when raising the top, after the tonneau lid opens, you hear a motor running, but the top doesn't start moving for about the same amount of time as the pause when lowering.

Ironically, or not. That amount of time is about how long it takes for a window to open/close.
Like it is waiting....

 

Drove home from pizza lunch with fellow Jaguar drivers and guess what the dreaded "HOOD NOT LATCHED" popped up. Oh well leave it parked up in garage while I go the SUPERCARS Gold Coast Races in Australia, will fix it when I get home!