Keep in mind for the 46RE, 46RH, 42RE, 518 etc, those transmission need throttle linkage to control the 1-2 and 2-3 shift. The 3-4 is controlled by the computer in the RE trans. 3-4 is done with pressure switches in the older RH transmissions via the PATC kit. You'll either need a cable driven throttle body or the Bouchillon Throttle pressure cable system. Or at least you'll need that to keep it a true automatic.

You can go to Cope transmission and get a manual valve body which simplifies things, but kind of defeats the point of an automatic trans. Cope can also steer you in the right direction to build the 42RE to handle additional power. 46RE seem to be fairly easily found at most pick and pull yards. The 46RH is a little more difficult as your talking 95 and earlier. If the Holley unit will control the RE, that seems to be the right choice.