TF really needs to redesign their links. I had this same issue when I first installed my TF kit. It was initially installed as a 4" kit w/3" springs, but is now set up w/4" springs. With the taller springs the links will just clear.
To make their somewhat universal sway bar link design work on the rear of the JK they move them to the inside of the sway bar & lower mount. If you mount them on the oterhside they'll hit the tires & rims due to their width. This can cause the problem you're experiencing, plus, unless there's enough bump stop to prevent it the upper joints on the rear links can hit the hard brake lines. As noted in another thread, if you don't have enough rear bump stop installed they can literally rip the hard lines off, leaving you with no rear brakes. I still have the TF links installed on my rig but plan to replace them with Poly's links, a better design all 'round.