i have found very few people that have done this swap. the 4v or 2v 5.4's are a more popular swap, but that's not how the cookie crumbled.
goal:
swap in the 5.4 for as cheap as possible, making no upgrades unless neccessary to replace said part anyways.
what i have:
*00 gt 5spd (stock)
*a low mileage 2005 3v 5.4 f-series truck motor, complete from oil pan to air filter, wiring harness, computer, fly. just lacks accessories, but i'm hoping to reuse some of my 4.6's.
i'm going into this swap nearly blind. my goal is bang-for-the-buck performance. this translates into i just want the motor in the car for now. suspension tuning/lightening the car/bolt-ons, etc. will have to wait a long time. i got the car (wrecked) for a total of 500$ and the 5.4 for 600$... are you getting the picture yet? btw anyone interested in a v10 triton motor?
so far i have a battery relocation kit i'll be installing when i return to cali. the battery is a truck battery with 700+ cca's so no problems there.
it turns out a 4" cowl won't cover the intake... the 5.4 is 6.5" taller than the 4.6. i'm still unsure what to do for a hood, but as the car is going in for paint relatively soon i'll have to address that before the motor swap beings. i have become decent at fiberglass repair and sculpting, so i may turn it into a mach 1 type shaker-ish looking hood and just cut my stock hood. i don't want a 6"+ rediculous hood on a slow daily driver.
Q's:
*the tb is fly by wire aka no cable. i understand that this will further complicate the swap and i would prefer a regular tb anyways. will this cause a complication with the computer to put a regular tb on?
*i'm replacing the motor mounts, but i want to know how the aftermarket ones differ from the stock replacements. and if the price difference is small enough to warrant buying the aftermarket ones.
*the tranny will bolt right up to the 5.4 as the 5.4s are just taller decked 4.6s, but is there anything in this dept. that i should know about? the fly is an 8 bolt btw not a 6 like stock.
*being that the engine is complete and has the computer and everything pretty much i'll need to get her at least running, would a custom tune be recommended? i imagine most reading this would respond that yes, of course, but keep in mind the tune would cost as much as what i got the motor for. and 365tq on 87 octane is plenty for me at this point! however, will the power curve be so tq-heavy and low revving that it'd make the car a pain to drive? i guess i will just have to find out... but if anyone has experience in this area, i'm all ears.
*will the stock cooling system be sufficient? the only change planned is a 55gpm meziere elec. water pump.
*will the oil pan fit w/ the stock k member?
i may keep this thread alive over time as i have more Q's, if anyone with experience or knowledge feels like advising. 
austin