Whilst it is reasonable to assume that both silencers are identical internally this may not be the case due to manufacturing differences or cock-ups.
By 'back pressure' what do you mean. I interpret this as the pressure waves reflected up and down the exhaust but I suspect you mean something else?
Lets start by reminding ourselves of the basic needs of a motor .
1) It need fuel mixed with air at the correct ratio.
2) It need a spark to occur at the correct time
3) It needs the inlet charge to be compressed before ignition.
Any one of the above may give the symptoms you describe.
I would assume that you have:
- Synchronised the carbs
- If the tamper proof plugs have been removed that the idle mixture screws are roughly set the same.
- With the motor at operating temperature and at idle turn the idle mixture screws to see if the idle speed alters (having noted their position from the check above). If one or more don't have an effect this would suggest a partial or fully plugged idle circuit. Try a carb cleaner first then do 'The shotgun'.
- Checked float heights.
- Checked for air leaks.
- Checked that all the jets are the same.
- Replace the spark plugs.
- Checked the condition of the ignition system and replaced old leads and plug caps.
- Run the bike in a dark but not enclosed space and look/ listen for signs of arcing from the HT system. A favorite place is the LH front cylinder arcing to the coolant hose clip.
- Check and adjust valve clearances.
- Perform a cylinder leakage test.
I'm sure there are a few things I have forgotten and that others will chime in with them.
Bottom line though (IMHO) is 'does the bike perform as expected?' If it does then surely your concern is academic?
Should you want to pursue this then any diagnosis here would be guesswork and I'm afraid you will need to get your hands dirty to find the answer.