Difficult to know what you mean exactly by 'clunk', but by hand a belt drive when built probably won't be overly free and smooth to be honest. For example, you may find that with the wheels on, turning one corner will result in the diff working (like there's a motor meshed if you like). As opposed to a shaft drive which would be pretty free from new. The belts will stretch as they wear in, so check your tension after each run initially.
You shouldn't really be able to mis-align the belts. If you were to get the diffs in the wrong way, it would be obvious it was wrong. Worth double checking the fences on the diff gear are the right way round - the chamfered edge should be pointing inwards, towards the teeth.
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