I've pressure washed my NSX and had no problems. The last time was about 10k miles ago. Now, I'm wondering if i did install the cover upside down.
Have you pulled the coils on the rear most bank towards the trunk? That is were I found my misfire problem. Took the coils out and dried they were fine, but I'm guess if you had them in there for a while they may have rusted & gone bad? I had my engine cover in place as well when I developed the problem.