Ordered a rear caliper fzs 1000

[mickvp]

they may physically fit, yes. but there will be no place to put the bolt through to hold them in. yours will be this style:

http://www.ebay.co.uk/itm/Yamaha-FZS-600...1208213174

which only has room for one pin. it appears they did indeed change the design when the change to foxeye was made.