Fun signal processing project and all the sampling problems sound typical. Unless this is just for your bike, given that some of the pokey fours run up to 15k rpm ~ 250Hz primary, I think it would be a lot easier to use a significantly higher sample rate and then treat in the digital domain. If you can recognise the engine speed and signal as a reliable pattern (use a digital PLL?) you might be able to subtract it and get more of the chassis signal left. As another poster pointed out, if you could do a motorway run with a high sample rate you have a good dataset to experiment with, including seeing how far you could downsample and still get appropriate sensitivity and selectivity.
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