I would question their "knuckle" replacement. The only time a knuckle would be bad is if it was bent. I've never had to replace one because it wore out, it just don't happen. Most repair shops when they can't figure out the correct problem they just make you replace everything thats in relation.
The trans issue, if the fluids are clean and it shifts good then let it go untill you actually have a problem. Not knowing your miles I would say it could be a bearing but don't worry about it yet. Again a shop trying to upsell some work.