Yeah the 4406 electric is the way to go. The wiring differences between the 2000 and your 2001 Job2 isn't that bad. If you have the pinouts for connectors C110, C115, C125,and C139 you will be ahead. C115 and C125 are for the mounty, and C110 and C139 for the Trac. You will need to modify the charging harness to the battery junction box, the mounty used a megafuse, where the Trac used 2 fusible links. You may also need to extend the wires on the AC high pressure switch as they are in different locations from the 4.0 to the 5.0. The oil pressure switch wire will also need to be moved from C139 to C110 on the Trac to match the C115 connector.
Basically you want to repin the Trac's C110 to match the mounty C115 connector, and repin the mounty C125 to match the Trac's C139 connector. I have done a lot of research on this swap for the 2001 model. There may be a couple wires you wont need in the C115 connector like for the message center and air suspension, and about 4 wires that you wont use on the C110 connector that have to do with PATS E. I believe though you may have to ground the starter relay for the swap as with the 5.0 it is grounded, but with the Trac Job2 the PCM was the ground to the starter for starter relay control.
I know you will need though the high pressure power steering hose, throttle and cruise cables, A/C high pressure hose, radiator and radiator hoses from the 5.0. You will have to decide which way you want to go with the VSS, if you want to swap the ABS module and g-switch from the mounty to the Trac which involves extra wiring or if you want to use an aftermarket calibrator like the Speed Changer II calibrator for the VSS signal. As for PATS you can do away with it in a tune, or you can transplant the PATS B components from the mounty to the Trac, but you will need to do some wiring under the dash. I have some notes and diagrams for this swap.