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Turned down length of mine were fine. It just meant I had to make taller idlers than I originally expected.
So you're saying that the pulleys have such a large diameter that they hit the horizontal frame members which support the bottom plate? How many teeth did they have? Up to 36 should be fine unless they have really tall rims. The 36T GT2 pulleys I used still had 8mm of clearance. Only gotcha would be if you used thicker vertical rails pushing things further back on one end.