About the conrod failure, no I don't think so, because normally you would see conrod failures if the head clearance is too low.... I think you just had bad luck with the conrod....
But maybe because of the big head clearance you needed to put in quite a hot plug to keep the engine running, which on his turn might do some harm... don't know....

I don't know the Ninja engine in detail, but 0.55mm head clearance without any shims installed seems a bit high to me...
It is possible offcourse, but most engines I've run, Nova based, Picco based, have a headclearance of somewhere between -0.5 to 0.25 mm (with -0.5 I mean that without any shim, the piston hits the headbutton)