Torque rod gone. With decent springs, no effect on braking. With lousy springs.... dunno.

FWIW, my shock tower bottoms are about even with the top of my IFS frame (SAS). I really don't believe there is a cookie-cutter approach to locating them; your best bet is to pick the longest shock possible (I run Rancho 99012s), flex your suspension full compressed, compress your shock ALMOST fully (leave a margin of error), then use that to position the shock tower on the frame. Remember, just fully compressed both sides (such as "with no springs" compressed) is not the fully compressed position for the shock in the real world. The shock resides outboard of the bumpstop, and with one side compressed and the other fully extended the shock tower will need to be higher than you might think otherwise.

Yes, my shock towers protrude through the inner fender into the engine compartment (no body lift). You will have some cutting to do.

Be SURE to brace the back of it with wings. I used 3/16" steel to do this. My braces mount to the top of the motor mount bracket and the back of the tower, and the lower inside of the tower is welded to the vertical portion of same bracket (which I had boxed closed and flush with the frame vertical face after cutting off all the IFS hoohaw). They have never moved, never cracked. Very solid.