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I have done exactly what you are asking.....
2000 996 3.4 to a 7.8 dme 3.6 x51 create motor......

you can do it but...being the 7.8 dme uses a different can system so some of the components in the cat will not work without upgrading the instrument clusterand such....

you will lose cruise control, and you'll need to convert the output from the heater control to turn on the a/c.

you'll need to use a later water temp sensor.....
you'll need to run 6 additional wires iirc....will have to look at my schematics....
also the later 3.6 uses a variable fuel pump, where the 3.4 has a regulator.....i used an aftermarket fpr with aeroquip fittings and lines....

overall there are about 24-28 changes in the pins of the dme/engine harness.....

the cust who owns this particular 996 had over 20,000 track miles on it when a rod broke and punctured the starter, I was handed his broken car, a crated 3.6 x51, a 7.8 dme, and told to make it work without breaking the budget.......the car currently has done a number of track days and is running strong....