Couple of things. First if it happens in big-big crosschaining it might be the chain is too short and the derailleur wants to shift down the cassette.
Second, you shouldn't change the missing-link mid chain life. The idea is the missing-link and chain will age and stretch together. If you install a new one on an old chain its pins having started stretching yet it will be shorter than every other link in the chain and can cause a clunk every revolution. http://sheldonbrown.com/chains.html
I would put on a new, corrrectly sized chain first, they cost what $30-40? if that doesn't work I would look at the following.
Third, have you checked the derailleur cable tension, is the cable housing "gummed up" if it hasn't been used in a while, is the derailleur hanger straight, was something leaning up against it over the winter?
Evo 5.63kg SL3 6.66 viewtopic.php?f=10&t=110579
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