Hi Oldsmobile_Mike,
If DiskSalv isn't helping then...
I think your gonna have to start over and I'de start by replacing that flakey keyboard first, then remove all the "junk" that you don't need.Then I would install Amiga OS 3.1 to a freshly prep'd HD, then once I had that all working without any added "junk"(software or hardware that is not necessary). Then once I knew that all is good, then I'd install 3.9 . Otherwise I think you'll continue to have problems. I'm sure someone here will be able to shed more light on what caused your problems. I just think your best off to cleanup your computer and start fresh, this way when something doesn't work it maybe the last thing added. Just my thoughts on it, I ain't no expert. Good luck with it, I'm sure your really gonna love 3.9 when you get it going. :-)