I've noticed on my Coupe that the fibreglass around the windscreen opening varies in thickness from say 3mm to 6mm+, especially in the corners (thicker). Do I need to remove this excess with a grinder/sander or will the windscreen rubber adapt to these iregularities.

Thicker body means better seal - it squashes the seal onto the body and glass better, plus, if it's anything like mine, you can get stress cracks at the corners, so keeping the thickness is a good idea.

Was just looking on the Wollies site for the rubber extrusion, my spec as below:

Front screen - 6mm glass, 2.5 - 4mm glassfibre edge
Rear screen - 3mm acrylic, 2.5 - 4.5mm glassfibre edge,

So now what size rubber do I go for

Part No. R399c = 6mm glass - 2.6 - 3.2mm panel
R606c = 6mm glass - 6mm panel

Obviously this is for the front screen only, but I was thinking that by the time the interior fabric is in place the panel would end up being around 6mm, any suggestions on which to use.

Sorry another question, can the extrusion be used either way (i.e. glass where the panel and vice versa), as I see Wollies don't do a rubber with a 3mm glass and 6mm panel?

Personally out of those two I'd go for <Part No. R399c = 6mm glass - 2.6 - 3.2mm panel>
The stuff I bought was certainly symetrical (apart from the gap of course) so I don't see why it wouldn't work both ways.