i have a similar issue going on now but mine is missfiring on cyl 3 because the mount broke on the intake, BUT my intake's leak has got 5X worse so i'm just going to throw a new intake on it this weekend..
as far as your problem, if it is in fact water getting on the coils, maybe its not the coils fault, have you checked the seal on the back side of the hood? or maybe check in the potential "splash area" around the wheel wells in the engine bay for a bare wire?
i'm not doubting your problem but my cylinder #1 plug & coil is swimming from my intake leak.. also, are you using motorcraft coils? cheap coils could also be a problem..