I tried removing the rear wheel as per the manual.

Remove the R clip, remove the nut, remove the shim, remover the spacer, remove the rear wheel........no wait!
scrub the last bit, its stuck and does not 'simply' pull away - has anyone had this problem, and if so, what did they do to overcome it?

Brute force!

when they changed my rear tyre on my old bike they put a block of wood on the tyre and a sledgehammer!! patience and muscle power mate

An alternative to a hammer is to level the wheel off. If you look closely it is possible to put a flat blade screw driver or similar between the edge of the wheel centre and the nuts holding the brake disc. Then level a bit, rotate to the next nut and lever again. Keep going around and eventually the wheel will work off. It can be slow but is effective and less violent. Once the wheel is off clear the drive pins and the centre and lubricate, should make it easier next time.

It also depends where the wheel has come from, a Honda wheel is easier to remove than an aftermarket one.

Although independent results may vary.

Gear puller was the least destructive for me, just be sure to pad the teeth with rubber, and lightly grease the hub when the wheel goes back on so its not such a dogshow the next time

Once you've levered, kicked or whatevered the wheel off, ream out the 4 mounting holes in the wheel, clean the the centre hole in the wheel with some 600 grit and then smear a bit of copper slip on the hub otherwise you'll be kicking it off next time as well.

decided to get a big gear puller - i'll make sure its all in good order before re-assembly though