Offhand, I'd say that it's not worth it.
In general, FE mods just from changing the "programming" in your car's computer will not be that large. It needs to run right around a specific air-to-fuel ratio (14.7:1) to keep the catalytic converter working, and the ECU in the car is set up to do just that. You can potentially cut down on some things (in general, that cuts into whatever "safety margins" the factory built in) but the gains will likely be small.
The cold-air intake will not help your FE. In fact, there's a decent chance it will reduce it! Most engines are more efficient when they are pulling in warm air, though there is definitely a point at which it gets "too warm". In the winter, it can be better to pull air from right next to the exhaust manifold!! Search "warm air intake" on here for examples and discussions of why.
I'm thinking that the pay-back on the $300 re-flash will be on the order of many years, unless fuel prices go through the roof. If they do, and if it really does improve your mileage, it might pay itself back eventually.
How you drive has a larger effect on your mileage than computer chips or air intakes. Read up on "eco-driving" or "hypermiling" to see the hows and whys. I've gone from 30 MPG to 47-48 MPG in my CRX Si, which is more than you'll see from any mod.
-soD
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