Well, I've got the bike back. They said they'd been through everything but couldn't find a fault. Said they checked throttle boddies, sparkplugs, air filter, HT leads, readjustment chain, changed petrol, put fuel cleaner through (still not removed tank??), reset timing, no error codes and spoke to Suzuki. It is running better though the judder is still present however the dealer said it's a mystery - could be chain/might not be. I can either change the chain and see if it fixes it, or they'll go to Suzuki to resolve the issue.
I'm guessing if they go to Suzuki and say they think it's the chain, Suzuki will say change the chain then? Anyway they're going to call me tomorrow to suggest what next. (oh, they still didn't fit the side panels correctly again despite me telling them this last time!)