So, manged to get myself a brilliant roof rack - very similar to the Safety Devices style. Bought from eBay for a good price, nightmare getting it courier here for other side of the country!
Seller had assured me it would fit properly and alow clearance for sunroofs - does look OK, only problem being it won't fit with roof rails in place - frustrating to say the least!!
So my options are sell it and buy another, probably not as nice (I think the contoured shape), rack that fits over the roof rails.
Or..
Remove the roof rails.
So, as I've got to get headlining out anyway and replace everything rear sunroof motor, it makes sense to remove roof rails.
Fine so far.
But where on earth do I find blanking caps? Or do I just use rubber grommets and some silicone?
Would rather it was a neat and tidy job AND THAT IT DOESN'T LEAK!
Anyone got any suggestions?

Just type "plastic blanking plugs" or rubber if you prefer in the search area of eBay and you will find loads in all sizes. Simple.

+1

Rubber blanking plugs or blind grommets should do the job quite adequately. If you'r really worried about leaks, you could try a smear of something like Silkaflex or Tigerseal in the groove in the grommet before you insert them.
Just be sure to obtain the correct size of grommet, too small and they won't seal. Too large and they'll wrinkle when they're inserted and then they could leak or even suffer damage when you push them into place.