I had a similar problem in an Honda Jazz automatic, went through everything, had an mobile mechanic come out plugged in the diagnostic unit and came up as misfire on cylinders 1 & 2, Suspected coils, wasn't that, changed ATF fluid, wasn't that. It only seemed to happen when engine was under strain, a hill or sudden acceleration. I put up with it for best part of a year. Then realised what may be going on. Just before the juddering started I had added some system cleaner to the fuel tank, i had less than a quarter of a tank of petrol in there at the time and the bottle of cleaner was meant to treat 2 full tanks worth. Long story short asked a local garage if it was possible to clean the injectors somehow and relayed current predicament. Im not entirely sure how they went about it but believe it involved undoing the pipes that go to the injectors and spraying some kind of cleaner in there. I think it was just a couple of hours labour. Did the trick, no more juddering up hills etc and mpg improved. The current theory is that me accidentally pouring way too much system cleaner into the tank with not much petrol in, had removed some deposits that were big enough to restrict the flow, but it would only be noticable when under strain. I know its a different vehicle but a partial block somewhere in the fuel intake region is certainly something to rule out before doing any serious surgery. Best of luck if its not already sorted.