I did a 3.8l Auto to a 4.6L cobra with 5 speed swap. Heres a list of parts you will need to swap transmissions.
Computer
Clutch Cable
Flywheel
Clutch
Transmission
Transmission Mount
Drive shaft
Clutch Pedal Assembly
Transmission Wiring Harness
Steering Column (It has a key release mechanism, almost like with the automatics how you cant remove the key with out it in park)
Transmission Tunnel (There is a layer that is spot welded on top of the original automatic tunnel that allows you to bolt the rubber shifter boot to the body)
Interior Shifter Surround
Here are some pics of the Transmission Tunnel I am talking about.