Luke there are going to be loads of opinions on this but here is my take;
Firstly you need a manual for your bike and a basic understanding of what is involved in a valve clearance check.
A copy of the factory manual can be downloaded on line but I would highly recommend the Clymer manual for the FZR600.
It is so near to the 400 (of which there is no hard copy manual in english) that it makes little difference; but mainly it is excellent for generally talking you thru a procedure;where the factory manual expects the reader to know the basics.
Here is a cheap copy;
http://www.ebay.co.uk/itm/Yamaha-FZR600 ... _71wt_1012
You can do the valves in the bike but it is awkward.
On the bench is much, much easier which is why when building them and the engine is out it is foolhardy not to check.
I know for a fact Boris does it this way also.
I use the compression tester to see if the valves are at least closing fully.
It is by no means a guaranteed method (too many other things influence the reading) but it can save major teardowns.
At this point you need to read Mang's thread "Won't start".
Here is a link to a shim job on a 400;
http://www.gtamotorcycle.com/archives/s ... -on-FZR400
Checking them is much less involved than actually having to change the shims.
online works manuals;
http://www.carlsalter.com/download.asp?p=1299
http://www.fzrarchives.com/ipb/index.ph ... opic=36294 (download all parts)
A red box doth not a Snap On make.