There are a few things that jump out at me..

One: the chokes on AT are rubbish.. they stick! I have completely disabled mine, pull of your tank and manually pull out your choke at the spring and see if this is the cause (I have money on it..).. It is likely to be stuck 1/2 open or closed or some other annoying thing that will screw up your bikes pull). It you can avoid using the choke to start on most days.. there is a modification where you can put in a heavier spring.. but this may be very hard to do on the road.

Two: it could be your fuel pump.. Are you running OEM (standard honda)? .. They go on AT at rate of about 100% mostly near the 20k mile mark .. make sure that you are getting a decent flow.. (do this by filling up tank and by passing fuel pump). Personally i would but a new Facet pump (£40) anyway.. yours will break sooner or later... It could just be showing the 1st signs..

Three:Check your plug leads that they are not cross arcing (in the dark. Rev engine and spray with plug leads with water if you see a spark you need new leads..) . or that your CDI is not gone bonk! (this i know no easy check).

Finally also do the standard ... clean air filters (and scoop.. most people forget the scoop).. new plugs.. good oil/filter. And yeah lose the petrol in your tank if it is mostly ETOH your bike wont run well.

Good luck

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2000 Africa Twin
http://two-up-ona-twin.blogspot.com