Well I think the problem's solved!! I just went over the stern 3 feet of the sheer panels with another coating of stain, then when I wiped it off, I ran it out forward in the direction of the original stain. When it dried, there was a nice fade in to the darker stain that ended at the back of the boat. The original mottled srew up area is barely noticeable by me from 3 feet so as far as I'm concerned I'm back in business without having to re-do the deck. Yeah!!

I would have darkened the entire panel except for the fact that there is a puzzle joint amidships that has already been sealed with epoxy. That part of the panel wouldn't have accepted any more stain and would have shown up if the areas on either side were stained darker.

Thanks everyone for all the good suggestions. Youse guys really helped be see I had more options that I had originally realized, even if it took me awhile to figure out the one that would work for me.