I've recently bought an '08 model 690 Enduro... When I initially looked at it... I was told the O2 sensor needed to be cleaned... mine also has an after market pipe, standard airbox though... and I was also told the fuel injector was cleaned...
1st day when I rode it, all was well... untill it started raining... then the thing absolutely refused to idle... Took it back - and was told they replaced my injector... since then - she seems to purr like a kitten.... (granted, an angry, extremely loud kitten....)
so perhaps cleaning the injector is also an option to look at? failing that - I have to admit - I have had nothing but epicly awesome service from the guys at RAD Moto...