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So, first thing I'll try is pre-loading the lever before I shift, and I think I'll up my RPM's from my 3500rpm target to 4-4500rpm's.
Of course there could be a problem, but if your clunk is mainly 1st to 2d, and not so much in other gears, then it is really the character of that transmission. An IPOD or earplugs helps a lot!
Also, shifting to 1st from second is a very clunky shift. I tend to stay in second even if there is a bit of lugging around 2000 RPM. I shift to 1st after or very near a complete stop.
My guess is all is fine.