Gas mileage loss after major service?

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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.
Great insight, thank you. I did forget to mention the throttle body sync, that was indeed done. As far as the TPS, that is over my head, but I will ask my buddy about that possibility.

 
Just to throw another fish on the fire----

If you still have it, check old air filter.

If it was really dirty you just increased your airflow significantly when you replaced it with a new one.

With fuel injection the ecu should compensate with additional fuel.

This means additional HP.

This is a good thing. :p

 
I am in almost the exact same boat,

TBS

Iridiums

K&N Air Filter

Went from 40-45MPG to less than 40MPG but I have to admit my wrist is some of the problem, it just runs so good I can't help myself!

I have started backing off on the interstate (I commute about 60 miles round trip everyday) since my MPG goes down significantly if I go over 80MPH. Hopefully my MPG will go back up after slowing down some, as if that was possible...

 
Since you're in Southern California, I doubt that this is an issue for you. But in much of the country we've seen drops in temperature and this could lead to raising a windshield from the low setting to the high setting. That'll give you a drop in mileage too.

 
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