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I have had the same experience on two occassions. First when I hadn't cleaned the air filter in maybe 30 000 km (yes, my bike doesn't get enough attention). You might want to double check the workshops work, and I also think that on roads like ours the filter can fill up quickly with dirt. Especially in winter, with lots of grease and sludge.
The second experience is right now, I have a problem with the charging so voltage is low. I thought it was the battery so replaced it, it wasn't the battery but the bike ran stronger for a while. So check your charging voltage, it's a simple test. The ECU should compensate for lower voltage but it seems it doesn't fully, or quickly enough when the voltage varies due to bad charging.
There are people reporting improved performance after valve adjustment, I don't understand how. When adjusting the valves you normally make them looser, meaning less valve lift and less duration. But we are talking very small differences, maybe 0.1 mm lower lift. In any case, the bike would be very slightly slower after adjustment at least at high revs.
A third possibility is that the spark plugs are worn out, you don't mention them. The original plugs shouldn't last more than 40000 km. The manual says to replace them every 12000 km.
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