stevenf, I will tell you my experience... maybe some of it will apply to your situation.
We build our house 20+ years ago and I got a metal roof because I wanted it to "last".
Well, the idiots that screwed the roofing down put the screws (yes, built for the purpose with washers under the heads) in the VALLEY of the material, not the PEAK of the corrugations. Corrugations are flat on top. I was distressed at the time but was assured that "that is the way it is done." Bull.... I've visited numerous countries in latin american rain forests... THERE they are smart... put the screws on top of the corrugations, not the bottom. As a result in our case, as the screws backed out of the underlying wood because of heat/cold/time, they began to leak. Lots of leaks.
I've tried several times to resolve the problem with repairs rather than replacement. So far, I've had to go over the roof 3 times, several years apart, removing loose screws, filling the underlying hole with black roofing caulk, then reinserting the screw into the hole and hoping that the caulk holds and fixes the problem.
What I have learned is that is is best to buy the very expensive caulk.. with silicone in it... so it will remain flexible...it also seems to bond better to the metal roof material and make a better water seal.
Some of the first caulking I used was more asphalt... it has dried out, pulled away from the tin and allowed leaks again at that point.
So, now I remove the screw, use an angle grinder with wire brush attachment to clean off the old tar, scarring the roof for an area as small as possible, maybe less than the size of a quarter. I force the caulking into the hole leaving a large dollop on the surface. I feel with the point of the screw for the old screw hole and using an electric drill reinsert the screw. I seek to just snug it down.... otherwise it will strip the wood hole, if that hasn't already happened. I make sure that the caulk closes over the head of the screw and spreads out to cover the wire brush marks.
Then, on to the next one.
In your case, I'd put a nail or screw into the .22 holes in the roof and cover them with caulking. As for the rusty places.... I dunno... maybe just paint them over with the asphalt roofing tar???? I don't know if this will decrease or increase the rust rate.
Best wishes!