Many thanks for everyone's comments. The twin carb manifold has an lip around the port, and a corresponding recess in the carb mounting. The spacers don't come with these recesses, suggesting they're not intended to be used ...? I've machined the recess into the spacers, so I'll give it a go and see what we get.
I've managed to drift out the brass jet body and found the pilot circuit recess, complete with 3 holes!, to be a bit grimy and blocked up, so hopefully the cleaning of that will resolve some of my issues - notably that winding the pilot screw in and out made no difference at all prior to cleaning!