I would also disagree with the tuner thing. I've never heard of a tuner who knows how to tune for a hypermiler; they get practice tuning for a few racers and many wannabe-racers. The OEM tune is most likely better for a hypermiler.
i have done plenty of MPG tunes. i like to throw a few cheap bolt-ons at the car, then some cbr injectors and tune for lean cruise. cbr injectors atomize fuel like you wouldnt believe. you can cruise at 17-18:1 afr with no problems. of course thats not the best for emissions and thats why the stock tune isnt best for MPG. they compromise emissions and MPG.
i have no clue why hondata doesnt list the po5 ecu, i have one in my racecar right now running neptune and i have probably sold at least 50 of them chipped.
also on your warm air intake. i know of the benefits of warming intake air and fuel, but i am a big fan of making horsepower and being efficient. have your cake and eat it too if you will. i have no problems getting single cam civics without opening the engine making 140whp and getting 40+mpg. thats the beauty of fuel injection. you can tune the cruise area of the map completely different than the high load acceleration area of the map.
An MPG tune for an average driver or racer/wannabe is not the same as an MPG tune for a hypermiler.
Bolt-ons rarely pay for themselves in MPG improvement, when measured accurately. If your goal is saving money then bolt-ons are usually counterproductive.
CAI vs. WAI: It really depends on the car. Some cars get better FE with a WAI (and worse with a CAI), some are completely unaffacted by IAT. The commonly cited issue of freeing up flow is a non-issue for an economy-minded driver, who uses a fraction of the available free flow in a stock system. A CAI will simply not improve FE for an economy-minded driver.
Certainly there are some things that can sacrifice emissions for FE. There's also things that might sacrifice some driveability, like more aggressive DFCO. The improved injectors allowing a leaner AFR sounds possible. How much does a tune + CBR injectors generally cost, and how much improvement do you think someone already getting 140%+ of EPA estimates will see?
Edit: And anyway, most fuel-injected cars come from the factory with a CAI.