You won't be able to drill the spot welds on the roof skin as the skin is roller welded on which is basically hundreds of smaller spot welds so close together that they almost touch.
If you go down the new skin route, you would need to remove the old skin by grinding out the roller welds. There is a bit about it here on a Mini that I am in the process of doing a roof skin on
http://www.theminifo...rage-iow/page-4
If you decide to try and split a used skin from the frame, you would need to use the same grinding process but on the underside of the gutters and then carefully split the roof from it but a new roof skin is not terribly expensive so not really worth the hassle especially when there is so much potential to destroy the edges of the skin when trying to split it.
If you are going to fit a used roof with the A, B and C pillars and join through the inner and outer pillars, then you will need to stagger the cuts and joins so that the outer skin join is a few inches above or below the inner skin join. This will give more strength.
However, I would remove the windscreen boxing panels and the top of the inner B post frame from the donor skin and leave these intact on your car. That way, you can get a more accurate cut and only have one join on each pillar.
Cheers
Ben