possible - the frequency of vibes could be different - everything vibrates at a particular frequency, and by changing the lengths of components you change the frequency - so yes, it's certainly possible that you feel it more. I'd ALSO check to make sure that when you moved things around, that you got the torque settings for all the bolts right, that nothing is touching a component that it shouldn't etc. Also check motor mount bolt and swing-arm bolt torque.
Seek, and ye shall find.
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