OK so now I've got my pancake air filter poking out through a nice neat hole in the bonnet. Trouble now is that the front of the carb (twin choke weber) fouls the bonnet, and the choke mechanism is also painfully close.

I don't think this would happen with a single choke carb. Suppose I've no choice but to shape the hole accordingly.

Anyone else find this to be the case?

Yep, me too. Although, the throttle linkage is clear. I just shaped the hole accordingly. Makes it look a little more interesting.

Mine was going to have an interesting hole, so I dropped the engine 20mm to get a nice air filter shape.

David