Re: Swapping a 4.6 into a 2006 V6
If you have a donor car it makes the swap a lot easier; even easier if it is coming from the same model year. No need to change the fuel pumps or motor mounts, everything is the same there. Get the 8.8 rear end, the 7.5 won't last.
You will need the computer from the donor car and a tune that disables PATS because things won't match up. There are miscellaneous bits and pieces you will need as well - most of which can be pulled from the donor car.
Several people over at mustangcollective.com have done the swap and there are some write ups on what you will need there.