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The spots that are not rusted through can be treated chemically. The others look to be fairly small. You can grind them to bare metal with a dremal type tool and a shop vac. Just keep your vacuum hose at the hole while you grind and you should be able to keep metal and rust from falling onto your liner. You should have a layer of insulating material between you roof metal and liner. I would then brush rust converter on the holes then plug them with two part epoxy putty. Then rust treat the whole roof, epoxy it, polyester skim coat then paint with at least two coats of primer sealer. When you apply your mastic for the vinyl make sure your roof is smooth and dust free. Any imperfections can cause pin holes in the vinyl and you will be replacing it again. Take care.
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