I have, but they were all cam related with the exception of one where the woodruff key broke and wallowed out the keyway on the end of the crank. None of those are "stroker" issues in my mind. If you are taking it apart, I wouldn't put it back together with a stock crank. Now whether or not you should leave there bottom end untouched is a different matter altogether IMHO.
What are you worried about being a weak point on the AMC I6? With your turbo setup and tuning ability, I would be tempted to slap an aluminum head on it and run it as is. But if this is your spare motor to build, and you want to build it, stroke it.