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You're in good shape. Try upgrading the firmware to v5.00 and my guess is that everything will work fine.
Yes, that's what I meant. You can always downgrade later if you want, although it's very unlikely that you'll have any reason to do so.
Please consult the eclipse troubleshooting page on the IOIO wiki.
And upgrade ADT to latest.
The simplest way to pass data between the main thread and the IOIO thread is to define member variables in your activity class that get shared between the two. All the example apps do that.