I have a 2003 altima that recently received a 6mt trans after being automatic from the beginning of its life as well a a 2006 M/T computer. The competed is wired into the 2003 A/T harness and pins were moved into what I believe are the correct locations. Most of the pins were a direct move to a new location but some powers and grounds were spliced into existing ones since they no longer have dedicated pins in the ecm.
This is an extremely difficult task, and involves taking wiring diagrams from the '03 vehicle, and the '06 drivetrain. Then mapping electrical power paths - power in "Start" position only, power in "Run/Start" etc. Then mapping sensors for the computer as you mention.
When I am involved with a swap like this, I put plywood on the walls, attach pegs to hang things from (both the vehicle and the drivetrain), grab some masking tape, and pens for attaching notes to wires, and start sorting it out on the board. When I'm convinced I have it right, then connect the bits in the car, and VERY carefully start applying power and checking for expected results. ECMs and TCMs are expensive.
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