Admire this!

Left side running super clean and weak or over advanced , right side looks pretty normal carbon deposit . Rings and bore working well but top ring on left side probably affected by mishap .

There has to be a reason for the weak LHS.  I would check needles against each other for length and diameter and ref no.. .check needle jets internal diameter (i use a tapered  knitting needle and compare length of entry ).measure main jets , Look for air leaks on spacers .Are Both silencers the same internally?. You  thought you  had bias  issues with siamese pipes , but perhaps you did not?. RH carb does not have a float chamber, when bike is banked over RH carb will steal all the fuel from left .Check flow from tap, catch fuel and calibrate . there is a minimum flow needed figure. Winning PR 650 was fitted with a bigger main on LHS ,probably to counter lube inequality. Leave out some treats for the fairies and gremlins !!.

It's risky to just fit new carburettors and ride around without going through the tuning procedure.

You shouldn't ride around not knowing whether your timing is correct on both cylinders, either.

As already said, you need fuel flow with a safety margin.  Measure it from both main jet cover holes at same time, with a gallon or less in the tank.

I don't think timing is the issue as Dave has already covered this and is well competent . This is something unusual and out of the box. I would be tempted to fit a single carb while running in again . The riding season beckons!

Piston damage from detonation and/or pre-ignition isn't nearly unusual enough!

Increase main jet size by increments of 20 until it's obviously too rich, then reduce by increments of 10 until correct.

Nobody mentioned spark plug heat range yet, unless I missed it, but it can cause holes in pistons.
 

I had a similar fright last year . In a  fruitless effort to eliminate an infrequent hiccup at just off idle I fitted new parts to my old carb , a new needle jet was slotted in. What I did not remember was that I had dropped the needle to compensate for the worn old jet . The mixture was now weak and a fast hard ride got the motor so hot that it would not stop when turned off , a diesel !!  I am convinced that it survived only because I was experimenting with expensive fully synthetic oil , extra slippery! . A new carb still did not solve the hiccup and only a refurbed distributor and a faster tickover made the difference.   And I still have not done a much needed plug chop  . !!

Fuel supply.   With a gallon or less in the tank I would expect a supply of at least a quarter pint per minute and preferably more for safety . 

Cam ring worn? check timing on both cylinders. Define 'hard running' were you wide open throttle? half throttle and loading the engine? etc

... I generally leave the main jet till last and always start with something a bit bigger than standard. The main jet only comes into operation at wide open throttle, and provided it's big enough I find setting slow running, cutaway and needle first means the bike is rideable for full throttle plug chops. Having said that I very rarely use full throttle anyway.