| Pro Twin, JHP, Tecmoto and Sigma are top notch and I would actually think that they charge more than Ducati Dealers. They have lots of experience tuning up Dukes for racing so I would be a little afraid that things might turn expensive with them.
But for general maintenance work, you do not need such specialists and the small independents are the best alternative as far as I am concerned. They are generally passionate people that know their stuff and love to do a good job. Not the trainee mechanic that some big workshops sometimes let loose on your bike!
The only problem with independant specialists is that you need to find a good one that knows his stuff and that has the tools for the job. Those guys will do a great job at reasonable price and this is why you should recommend them when you happen to meet one of them! | 
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