According to :

My plan is to get new screws, and replace the screws where the wood
will hold the screw. Where the wood won't hold a screw, I plan on going
a little up & down the pitch (a few inches) and putting in a screw.

My question is, for the spots where the wood won't hold a screw, should
I put a bunch of roofing spooge on a new screw and shove it in the
hole, or should I fill the hole with silocone or roofing spooge?

Also, what is the likelyhood that water is migrating backwards up the
lap joint?
If its likely, should I raise the top panel slightly and apply roofing
spooge between the panels, or should I just apply some spooge over the
top of the joint? Ditto ques. for sealing tape (which I hope was used
in the 1st place...)

With such a low pitch, and especially if you're in snow country, I'd
assume that the water is wicking back up between the panels.

If you're not going to pull the panels, you're going to need to seal
_everything_ you can (with at least a 2 inch band under the overlap),
and probably goop the new fasteners you install. I think roofing
goop is the stuff to use, the silicone will fail. You have to get
the upper panel lower edge solidly anchored/sealed to the lower panel
with something that has some give.

Likely part of your problem is the upper panel "working" against the lower,
and wrecking the seals on the screws.
--
Chris Lewis, Una confibula non set est
It's not just anyone who gets a Starship Cruiser class named after them.