I just adjusted the valves on my wife's bike.
Go to this thread if you want to see it... http://www.ex-500.com/index.php/topic,82.165.html
I did notice one major difference between the manual and the instructions on this site. I have the "real" Kawasaki shop manual for the EN400/450 and the supplement for the EX500.
The manual says to turn the crank to the T or C mark for TDC and the lobes should be pointing up and away from the rocker depending on which cyclinder you are working on. The site instructions say turn it to T or F. I used the F mark and not the C because the lobes were pointing in the right direction using the F.
Also, I noticed when setting the crank at the F mark to do the valves on cylinder #1 (cylinder on the right when sitting on the bike but the manual says this is cylinder #2!!), it had a tendancy to want to roll easily past the F. Wasn't too difficult to hold it on the F, but more of an annoyance. Easy to do though.
Oh, one more thing; maybe call it a tip or hint. Since the valves have a range of clearances pretty close to each other, you will only need 3 feeler gauges - .005", .007", .009". I loosened the adjuster and inserted the larger of the 2 feelers required (depending on intake or exhaust), adjusted until there was very, very slight resistance on the feeler when trying to remove it and tightened the screw and locknut with the feeler still in place. I did this because I noticed when tightening the lock nut there is a slight tendancy to "turn in" or decrease the clearance. Once adjusted and locked in, I removed the larger feeler and remeasured with the smaller of the 2 feeler gauges - it slid right in as expected.
This saved me a load of time and was able to do the valves in about an hour.