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I like your project and wish you success with it.
You might look at the Graves Motorsport Flash Tune ECU kit that lets you change the map in the stock 300 Ninja ECU, I'm not sure if they've got one for the EFI-equipped 250s. I think this is what a friend who is building up a 300 Ninja road racer decided to use. About $425 or so and it may be easier to get working than starting with the Ecotrons/MegaSquirt stuff.
Have you considered that your wire wheels will see a lot more side load than they would on a motorcycle? Sidecar outfits have that issue too, the spokes have to be stiffer/stronger to resist the side loads. Perhaps you are using wider than usual hubs to get a broader base at the spoke flange?
I look forward to reading about your continued progress.
cheers,
Michael
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