Do you happen to know much about waterproofing a sheet metal roof? I have an old barn building with one, but it drips from half the roofing screws in there. When I get time I plan to replace the screws, but I'm not convinced the old timbers will allow a waterproof seal...
The timbers shouldn't have anything to do with the waterproofing if the roof is in good shape. If you're worried about the current timbers not holding the screws (which I think that's what your concern is) then try longer screws. I would imagine the current screws are .75" to 1.25", just add another 1/2" or 3/4" and screw them in. Clearly, you should use the proper rubber gasketed screws