Okay, so it turns out the accelerator pumps weren't quite working as much as they should have so I've now set them to deliver the most they can on both carbs. That seems to have cleared up some of the spluttering.
I installed some 140 mains and 70 pilot jets but I'm sill getting a lot of bogging down low, I'm convinced it still has something to do with the primary circuit.
Tomorrow I'm going for bigger pilot jets again.
Does anyone else run these types of carbs or have any suggestions to the jetting arrangement?