Get one of the later 3-valve 4.6L motors - I think anything earlier than midway through the 2008 production run used a spark plug design that is apt to break (leaving part of it still in the head) when you try to remove it. Grab everything from the donor car - engine, 5R55 transmission, ECM, and as much of the harness as you can.
I can't help you much about the axle, except to recommend an 8.8 simply because it's still in production. With a normally aspirated 4.6L engine in a lightweight street rod, you shouldn't ever need anything stronger than that. If the S197 rear axle is too wide for your project, would you consider getting it narrowed (and get to keep the S197's rear disc brakes)? If so, grab that from the donor car as well.
Mine: '08 GT, 5-speed manual, engine stockish, suspension unstockish
Hers: '10 Subaru Legacy 2.5GT, 6-speed manual
Winter/Spare: '01 Maxima, 5-speed manual
Ex-winter/spare/autocross, now at a new address: '95 Mazda 626 V6/5-speed manual