Since your tire pressures are the same now as before, it may not account for the loss.... however, by all accounts, you would probably get some improvements if you were to bump them both up by about 5 psi. That's a lot in the grand scheme of tire pressures.
The other thing is that I've re-read the post, and I don't see anywhere in here where a throttle body synch was done.
I'm not usually a big fan of random throttle body synchs without specific reasons for doing them.... but when you make valve shim changes, you do give yourself a specific reason for checking and possibly rebalancing the throttle bodies.
A throttle body synch is supposed to match up the air flows into the four cylinders so that at a common throttle position all four cylinders are getting close to the same amount of air.
When you change your valve clearances, you make very small changes in your cam timing, but at the high speeds, these subtle changes could impact volumetric efficiency, and I wonder if you would find your gas mileage back again if this were carefully done.
The fact that you do not mention any engine vibration or roughness sort of discounts this theory though.
The other thing that can impact fuel mileage on a service is if the throttle position setting has been changed so that the engine control module is going into a different part of the fuel map as the physical throttle is moved through its space. On the Moto Guzzi Norge, they were notorious for coming from the factory so that closed put you into the table at 4.1% when closed was supposed to be about half a point higher. At WOT, the half percent at closed throttle was several percent and it had an impact on drivability, perceived smoothness, power, etc. If the TPS were changed, then for a given real throttle position the ecm/ecu is looking at a different part of the table than it was before, it could effect fuel economy, even as it made the bike seem to run "better."
These ideas may seem like a stretch, but you've excluded a lot of the other more obvious issues.