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Sorry - just saw this. There is no single place to measure.
As you note there is the alternator and battery. When the engine is stopped all current can be measured at the battery ground strap. But when the engine is running and the alternator generating you no longer have battery voltage - you have system voltage (including at the battery) which is controlled mostly by the alternator. There will be some charge current into the battery (most likely) in the reverse direction as when the battery is supplying current. The current at the battery negative will be just the battery charge current. The return current to the alternator (most of the system current) goes to its grounded case connection which is bolted to the engine block and not separately measurable. Your best bet for measuring total current is a clamp meter around a pigtail connected between the alternator main terminal and the alternator normal connections (usually 2: I to jum posts and one the the starter).
Yup, my first Motorcycle was a 1993 CBR900RR Fireblade (in Germany)... that is where the name is came from a long time ago!
It was good meeting you at the breakfast!