Surely the replacement ones are advanced enough to let it run fine, it's not like a Honda or many other more modern bikes where you have the immobiliser wired through them is it?
How about some R1 clocks etc - probably the thing here is getting the rev counter in synch?
I looked into this when I replaced the clocks on my R1 streetfighter. Your bike SHOULD run ok, but I'm not sure about everything working if you fit R1 clocks. The 4xv is the closest model to the fzs, but the clocks are crap!
I went through 3 sets of clocks in just over 6 years before buying a KOSO clock. I think mine was the RX1n. That would work brilliantly on the thou 8)