Well a stiff link would be most noticeable in the smallest ring (according to Sheldon Brown). Honestly, I have no experience with bad links other than when my BF broke a link on a brand new chain, but then I could see one plate sticking out, making a click sound each time it went through the wheels in the derailleur.

That it shifts and rides fine in the small cogs while you're in the big ring does tell me that your H limit screw is set right and that your cassette is probably ok.

I'm thinking that maybe your chain is probably getting too old for you to be cross chaining in the middle ring, even if it is harder to really cross chain on a triple. Next, instead of shifting up to the big ring, try using a little FD trim when you want to use the small cogs/middle ring combo (like a 1/2 shift with the front shifter). See what happens.