The 4T65e behind the LS4 was never considered to be a reliable trans. There were multiple issues that have been noted since the powertrains inception.
Do some research on the reliability problems that were found.
Better get the '06 transmission, too.
One wonders if you could swap the entire subframe--engine, trans, suspension, front brakes, steering, plus enough of the wire harness and the computer to make it all work.
If one updates the older caliper to the newer design one must also make use of the later rotor for the 94+ caliper. One cannot mix & match *old* with *new*.