Hi Andy,
I don't have a clymer manual, but i understand what they are wanting you to do. What they are testing is the average recharge current going back into the battery when the engine is running. You should find the red/white cable around your fuse box somewhere (perhaps behind it). One way to measure the charge current is to disconnect the red from the red/white and put the multimeter in between them (ensuring your multimeter is in amps/current mode and connected correctly). Then check what the current draw is against the book at say 4000 rpms. This is the average current that the rectifier is feeding back to the battery.
By all means you can run the above test, but it might be easier to start off with a general test instead by simply checking the voltage across the battery when running.
Before starting this test, measure the voltage across your battery and make note of it with everything off. I.e. Just to get a snapshot of your battery voltage which should be ~ 12.5v if your battery is good.
With the multimeter still connected to the battery measuring the voltage, start the bike up & run it at the following revs and make note of the voltage you see at each rpm snapshot. If everything is working correctly you should have something like this.
1000 rpms, ~12v to 12.5v
2000 rpms. ~12.8 to 13.2v
3000 rpms. ~13.5v
4000 rpms and above. ~14.5v (then maxed out at 14.5v)
Open this pdf file
http://www.hondachopper.com/garage/troubleshooting_charging_system/troubleshooting_charging_system.pdfand check out page 2
If your charging system is doing this, then you are probably ok. If not, then there is a screw you can play with on the regulator to correct it (assuming your system is ok). When checking at each rpms, the figures should be close to with 0.5v of that shown above, they don't have to be exact. Whats important is that the volts climb and max out at 14.5 volts over that rpm range.
Note: The above description only applies if your charging system is actaully working, but just out of regulation. If you have a problem with your charging system, like bad connections to the stator / field coils, bad diodes in the rectifier, etc. Then we will need to dig deeper to isolate the problem which will be another post.
Short riding runs on the bike can also take a lot out of the battery & sufficient ride time (say ~10 to 15mins) is needed to restore what you lost from the battery due to electric startup. The reason why bikes charge like this is to allow the bike to charge sufficiently for average riding, without overcharging (which kills batteries) or leaving you with a flat battery.
These bikes have very simple circuits, and with a bit of divide and conquer, you can get it charging correctly.