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Never underestimate the power of your processor. Make generous use of the timer interrupts, and feel free to run them FAST as long as you aren't doing long arduous calculations. Main loop doesn't make things run faster than if they were in a timer interrupt.
If you have an easy way (pre-written driver?) to burn values into eprom, you could do the exact same method as above, but instead of pipe the array out the serial port, you could just copy it to eprom, bring it to the computer and carry on from there.
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