Bad Charging on Navigator

They don't charge at tickover rpm!

Idling discharges the battery.  A battery with greater amp hour capacity will keep it ticking over longer, but will still eventually get too flat.

That's Normal !  Although mine doesn't stall but I dont leave it ticking over for 15 mins!
Dan 

The battery is either flat or not connected.

Nothing to do with 'wringing the throttle' a 5Ahr battery if charged will run the bike on tickover with no charging for at least an hour. The battery is flat when you start this bike or far too small for the machine.

Or it's a failing battery, which appears to charge but has lost its storage capacity.

The AC generated by Lucas and Wipac alternators have no meaningful output you can measure (with our cheap meters). At any speed. You can try measuring the DC voltage at the rectifier (NOT alt/reg) but as soon as you load it  will have an unknown result-depends entirely on the state of the magnets and the revs. And of course the state of charge of the battery you are trying to use to run the bike and be charged at the same time.
A one year old 5AHr should be ok to run this bike IF it is charged in the first place.
This bike should have 12V or a bit more at the battery just above tickover. If it has a rectifier then it should be fitted with a Zener (as a regulator) so there is the chance that the rectifier is faulty.

At idle they generate very little.  Sometimes the alternator can power electronic ignition with lights off at under 1,000 rpm, sometimes not: it's marginal!

It's what was accepted at the time.  Headlights were only used on the open road, when it was so dark that they were needed to see your way.

On lit streets, it's more likely that the pilot light would be used.

Points ignition would keep working even if the battery got very low.

... so how does the emergency start facility work?

The emergency start on the 6V alternator systems (using original alternator switching as regulation) puts the full output of the alternator to the ignition sytem, and with a bit of luck you get a start. One system even put the alternator output direct to points, (horrible but might have worked). 50 yrs on the wiring is tired, the connectors are even more tired, the magnets are getting weaker, but if your 6V original Emergency works, then what a lucky chap you are.

"At idle they generate very little. ....

... so how does the emergency start facility work?"

I've had bikes that would start and run splutteringly on EMG and I've had bikes that wouldn't start on that setting.

I've read Lucas' own description of the emergency start system and failed to understand it, so I can't explain it well, but part of the principle is to exclude all loads except the ignition.

As Alan says, I think sometimes they bypassed the voltage drop of the rectifier.

.. but I was responding to the statement that there was no output at idle speed (which is of course significantly faster than kickstart speed!).

I do understand how the 2 level alternator "regulation" is achieved which is why I've changed it on all the bikes originally fitted with it to a Zener regulated system.

There isn't "no output" at idle rpm.  There's (usually) no charge to the battery at idle rpm because the alternator output doesn't reach a high enough voltage.