I mounted 2006 40/20/40 seats in the front AND rear of my 2000 crew cab. I also added power tracks to both front seats (they were manual). They will definately bolt down in the same locations. I had to drill and tap the factory mounted rear sheetmetal bungs (they look like thick washers welded to the floorpan from under the truck) for the rear seats.
To answer your question, I would keep the power seat tracks already in your truck and swap the seats by unbolting them from the tracks-that will save your wiring headache except for the seat heater. For the heater, (which I am assuming has its own pigtail) you can probably just run a fused link from 12v ignition hot and a wiring pigtail can be bought at ford so it clips into the socket at the seat. In my application, I had to reuse the original seatbelt click releases because the ones on the '06's were different, but they are easily removed. So, in a nut shell, the swap is straight forward with the only custom part being the heater. For what its worth, this one of my favorite mods to my truck as the 1999-2001 seats SUCK!!
BTW-Even your old seats and/or the power tracks will pull a good amount of money on ebay or craigslist. Adding power seats/leather seats is a fairly common upgrade even if the seats are worn, so you should be able to recoup some of your money for the swap.
In case you don't already know, the mounting bolts are a Torx T55+ which is a fairly un-common (hard to find unless you know the snap-on guy) torx bit size. However, a much more common T55 bit works very well although it is a loose fit so be careful.
