Thanks Plumbbob, we've tried both sizes of the wire link and even with the shorter one it still comes up higher than the lid, albeit by less. I'll maybe talk to the manufacturer to see if they have encountered this problem before and if so, how they solved it. But thanks so much for your help, I'm really grateful for your time.
I have seen this problem before, but have always been able to overcome it by fiddling with the link and lever. If you shorten the link by bending it and by possibly hooking it into a different hole in the handle arm, you can get it to flush without the lever being turned to a degree where it contacts the lid.
Any extra length in the lever can also be cut off which will reduce the possibility of it hitting the lid.