I have a Royal Enfield Electra 500 lean burn. Which has 14,000 miles on the clock. Ive recently noticed a metallic clanking sound which is most prominant when the engine is idling. I cant be certain but the noise seems to be coming from the upper cylinder.Can you advise what the problem might be? Thanks

have a bike electrician check it out
I suspect that there is problem relay/regulator in the charging circuit that is allowing the alternator/generator to keep supplying power to the ignition outside the ignition switch circuit
could be a shorted wire
The dead batteries indicates this by discharging through the same fault.

W/ EPA regs they run HOT also w/ a cat in the headpipe. Heat..get a TFI fuler to add fuel.. the sound your hearing is pinging..also get a freeer flowing air cleaner K&N..

In order to run smoothly an engine must have the correct air/fuel ratio and the correct ignition timing.

A lean air/fuel mixture and/or advanced ignition timing can have a very big effect on the smoothness of an engine...

Have a look here http://royal-enfield.com/
I don't know your location so this is the main web address, from it you will be directed to an authorised dealer.
Hope this helps.

Fuel filter.
Fuel tank vent.

I have TB and I also had similar problem, expended almost 6000 bucks on fixing but nothing helped me. Then I got the half engine changed so that engine number should be same as in RC. Now it have cast iron engine on to and half AVL, it runs gud, have nice traditional sound, without any sound , no maintenance (if I companre with AVL), consume more fuel (who cares?) all in all it runs like royal.

But remember its a tough job and U need a gud expert for this who had earlier done this. If you need any help you can contact me.

they are right the mach 500 is a bone shaker