Swap intake manifolds from the 5.3 to the 6.0 to retain your drive by cable.
4L80e crossmember is sold by speedengineering, they do good work.
Whipple and maggies are a bit different. I can't remember exactly the difference, one is a roots and one is a PD(?) but basically one makes power a bit differently than the other. My uncle has an old Whipple on his truck that he likes.
Junk the ecu and harness. You cannot use them and won't need them.
Just go to a driveshaft shop and tell them what you want. They will cut that one down for you.
Don't forget to use the 6.0 fuel injectors.
Some sensors on the 2005 may not work with the 2001 harness. Those are easily swappable, I believe the oil pressure sensor is one and the alternator may not work as well.