MM, I've used Migration Assistant most successfully twice now and haven't had a problem. Everything has come over. I guess my only gripe (if you can call it that) is that I didn't really want everything and had to dump some docs and pictures from the laptop. 
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After transfer, will the Mac Pro have 10.5.1 or a new 10.5.2?
Sorry, can't answer this as I never used it to transfer the entire system.