I am pretty sure the metal bits ended up on the road with the previous valve cover. But nobody can say for sure. I have given the bike several oil changes and I haven't come up with any metal shavings or larger bits. Not to say they are just sitting in there, but I haven't run into them yet. I'm not to worried about it since I've put about 11k on the bike so far with only regular maintanence issues. Until I took off the valve cover that is
Once I got my valve cover back on thanks to that little helicoil. I found out that my cooling fins were bent and I couldn't get a seal.
So I bought some Gasket maker, and I sandwiched the gasket with a bunch of the goop and gave it another coating all the way around.

It seems to have worked out alright. I haven't started it up yet. I won't do that until tomorrow since I want the gasket goop to cure 100% before putting stress on it.
So this wasn't exactly the issues I expected to run into when I decided to adjust my rockers and valve. But adapt and overcome is all we can really do.
Thanks for the help. I will post later to let everyone know whether or not my gasket maker works out as well as I think it will.