in an ideal world you should have marked the gears so that they line up on the same teeth again. however not doing this won't result in a clunk, maybe some gear noise but not a clunk. a clunk indicates something is either loose or moving when under load.
minispools are natoriously hard on suspension bushes, if you have any that were in poor condition with the standard diff, fitting the minispool will show em up straight away. you mentioned it did a simmilar clunk when doing reverse burnouts

i'd suggest the problem was there before however with the standard diff it wasn't creating enough load under "normal" conditions to cause the noise
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VN exec T5: 15.1sec @92.2mph 1/4 mile, 9.7sec @ 74.6mph 1/8mile, 2.3sec 60ft, 0-60mph 6.827sec 22/11/07 Gtech competition