Definitely sounds like the carbs are out of balance, boxer engines are particularly sensitive to this. There's a few approaches to setting balance and synchronisation but what you are aiming to achieve is:
1, Both carbs flowing the same amount at tick over (best checked with vacuum gauges).
2, Both throttles are synchronised, i.e. the cables are adjusted so that both throttles start to open at exactly the same time.
Set up as follows:
1, Ensure all other sevice parameters are OK before messing with the carbs. E.G. valve clearances, ignition timing, plugs & air filter. Check basic carburretor settings are correct e.g. mixture screw basic settings, diaphragms in good order etc.
2, Get the bike thoroughy warmed up to normal operating temperature. Going for a run is the best way.
3, Slacken the throttle cables right off to ensure both carbs are controlled by the throttle stop screws only. Hook up a pair of vacuum gauges and adjust the throttle stop screws in & out to achieve the most even vacuum readings possible (they will almost never be pefectly the same) & the correct tick over speed for your model. If you've got a Colourtune or gas analyser now is the time to tweak the mixture screws to get the CO readings correct. You may need to re-adjust the throttle stops & mixture screws a couple of times to get the best compromise of mixture setting, balanced vac readings and correct tick over speed. If you're happy with the way the bike runs and the plug colour is OK don't worry about the mixture setting just balance the throttle stops. If you haven't got vac gauges you can do a quick and dirty balance by pulling of each plug cap in turn and comparing the idle (or how many beats it takes to stall) on one pot at a time. When they match go back to running on both pots and tweak each screw exactly the same amount until the correct tickover speed is reached. (Not the recommended method but better that nothing!) What ever you do don't let the bike idle for prolonged period as it will overheat.
4, When you are happy with the idle speed and balance switch off and adjust the throttle cables until each butterfly starts to move at exactly the same time. Sometimes easier said than done on a boxer unless you have an assistant tweak the throttle whilst you feel for the butterfly arms moving. Once you're happy lock everything up and recheck, remember to leave a little freeplay in the main cable so turning from lock to lock etc. does not affect tick over.
I hope all that does not sound too complicated. If you are clear about what you are trying to achieve and methodical in your approach it's easier to do than to describe!
Let us know how you get on...
First rides on 101 and i'm a little baffled. When i bought her she was as smooth as silk but on the ride into work today i thought id got a miss fire at just about 1000rpm, very strange as it feels and sounds like a miss but throttle responce is sharp, no hesitation she just pulls like a train. the other thing is tick over is all to pot. now i've not done anything other than change the throttle cables to a two into one arrangment and i'm wondering if i need to re-ajust the cables or throttle stops as the tickover may have just been set on the cables. all very quirky stuff but she's right good fun to ride. i'm getting altitude sickness due to the seat height and she's very sharp stearing which is a suprise. love it though, and i recon she'll be awsome off road
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