Check out the RPS V8 board. We have all kinds of info on there for 98+ swaps. There are some uniquenesses with each model year and you will be the first 2006 I know of. A complete 1999-2001 Explorer V8 will be the best basis to work from. You need so many parts from the explorer, that it makes sense to find a complete donor to work from. Try to find a rollover or rear end / side total job on eBay or similar.
As for stock drivetrain, only able to keep the front and rear ends, unless you use the Advance Adaptors kit to use the 4405 t-case from your truck. I would recommend against it. Too weak. Use a 4406 from expedition and have new shafts made.
ON the RPS board, there are a couple of stickys for the late model swaps. Read through those and do some searches for late model or explorer swaps. Once you have done your homework with those threads, post with questions of specifics you are un-clear on. We should be able to make this go smoothly.
I did my swap in 3 weeks. I have heard of it being done in as quick as 10 hours! The electrical system changes in the newer trucks have thrown some monkey wrenches in the works, but nothing too diffiucult to over come. Also the power steering line is no longer interchangeable for the Explorer V8 and the 2001+ Rangers.
DD: 2010 Sport Trac Adrenalin. 4.6L V8 / AWD with Terra Grapplers and Voxx G-FX wheels.
Toy: 1999 Ranger 4x4 4Door. Replacing 302w 1.5L Kenne Bell with a 351W: Explorer EEC-V DIS, AFR205 heads, custom 1 3/4" long tube headers and Autorotor 2.6L supercharger, intercooled with '03 Cobra and custom fabricated manifold.