Colin - absolutely right about the screwdriver approach, but at least it was an old one with rounded off corners! I've done a few MGBGT screens in my time and my weapon of choice for that job was a stainless steel dental tooth lifter!
Jon has now finished the job, so here are the follow up photos:
The strips have been gently countersunk to take the stainless cross-head setscrews.

This shows the original screw, the stainless replacement, and
a domestic socket screw - nickel plated brass which could be used if shortened.
Finally, Jon used a credit card to refit the rubber strip, a much better idea than a screwdriver. I'm really annoyed that I didn't think of this because I keep a couple of old RAC cards in the garage for just such a job! Grrrr.

Finally in Jon's words:
When re-fitting I coated the back of the channel with Waxoil & bolted it all in place then ran some more Waxoil into the channel & used this as corrosion protection & a lube to help refit the rubber insert – the tip with this is to tuck the shaped end in, hold the back edge of the rubber strip tightly down, then just run the edge if an old credit card along to ease the lip into place – looks messy but it all cleans up very easily afterwards. Another tip is to coat one face of the ‘penny washers’ with Waxoil a day or two before re-assembly – this helps them stick to the underside of the running boards whilst you fiddle to get the nut threaded, works a treat J