I really don't know what the impact will be on engine life. I'll be anxious to hear Bubba, wsa11 and others weigh in on the .003 clearance. These guys have far more real world experience - they'll know what you can get by with, versus what is ideal. That extra thousandth may not be a huge deal. I'm sure someone has some insight into this.
As far as the last two items on Bubba's list, cam bearings are possible, but for some reason I don't think they're likely. Not sure why I say that, maybe because there isn't any easy way to check them. I've never taken apart an engine that had significant wear on the cam bearings, but it does happen. More often I've seen them damaged from junk in the oil. Since you haven't really found any chunks of metal laying inside your pan, maybe the cam bearings are a good gamble.
On the galley plugs, if one was missing, I think the oil pressure would be ZERO, even at start-up. A plug could be cross-threaded or not fully tightened, so that's possibility I guess. Anyone have a list of how many and where all the plugs are? I know some are relatively easy to access, but others, not so much.
At this time, I'm thinking that maybe it's time to button it back up, cross all our fingers and hope that the big issue was the oil pump mount.
-Stu