If you coupled the output with a good quality high voltage capacitor you should be fairly safe....
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any idea what pentodes they used? If 807's as in colossus, good for 10MHz easily.
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I bet ERNIE didn't have any sort of A/D - they must have used thresholds. Not very random?
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if you stick with your a/d idea I think you're worrying unduly about the effect of your pwm/meter output - the arduino analog input will be driven by quite a low impedance from your pentode amplifiers. Check the anode impedance of your pentodes - it'll be a few k ohms .
regards
Allan