Right, I've linked the two points JP14 JP15 with a small wire for now, and replaced the caps noted above.
The ports are now both able to power up the Brook SD adapter and respond to D-pad and buttons ok while in analog mode.
I'll replace the jumper wires with 0-ohm resistors and likely do the same for the emi filters at some point.
Not able to fully test the controller in game at this time as this would require a full switch of another working system.
But it's certainly doing a lot more than it was, For now I'll call this a fix/win/solution.
Perhaps I'll get lucky and can grab a model 1 case, throw an ODE in it and bring it back into use.
I fear it wouldn't survive for long in the wild again given the failed 60hz broken pad trace job it came to me with.
Job Done....Finally