How exactly does a ball joint "wear in?" That is completely counterintuitive. Think about it- new ball joints tighten everything up; old, worn ball joints are loose and sloppy, which is the condition you're describing.
I'm not trying to be a dick or anything, but, as Tom said above, I've never heard of a ball joint "wearing in."
And that 3.5" lift is going to require a bunch of additional parts- adjustable control arms, adjustable track bars and, likely, new shocks. Possibly even new driveshafts depending on the geometry.
Not to mention a regear to get the power band back in it’s proper neighborhood with the larger tires.