Is the part in the link below the BB spacer that sits on the threads of the cups or is it the elastometer bit that sits on the axel for preloading the bearings? The instructions say they should be in various sizes, is that correct? In which case do i need to order all three?

http://www.chainreactioncycles.com/Models.aspx?ModelID=29489

Have a look here
It looks like the single spacer that goes on the BB spindle on the drive side. BB spacers are 2.5mm and smooth surfaced. It’s therefore neither of the things you’ve mentioned.

sorry, “rubber coated plastic spacer” the bit inside the cank is the elastometer. I installed it a few weeks ago, it didnt lok like it was on properly so i presumed it needed another spacer, havent got it to hand so cant see if theres a 2.5 or a 3.5mm elastometer in there.

Did shiomano realy patent the only sensible system?

It’s dead easy, just follow the instructions. I’ve been running two sets for a couple of years without problems – even the BB’s are wearing quite well.
Trust me I’m no engineer.

Forget the elastomer size, unless you start to have problems.
Spacers – extra one if BB shell is 68mm.