Yeah, they're the same motor, the 5.4 just has a higher deck in the block and more stroke for the extra displacement. The spark plug issues with the 2v motors was fixed by adding threads in like 2002/2003, but if you torque the plugs correctly on the older ones you'll be fine. To be clear it's the spark plugs blowing out, not getting stuck and breaking problem on the 2vs.
As far as the transmissions go, some have 4r70w and some have 4r100, the 100s are just a little heavier duty, I'm not 100% sure what decides which the truck will have, but they're both pretty good transmissions and will hold up to towing. 5.4s also have a 9.75 rear and the 4.6s have 8.8 rears. Not that it makes much difference, the 8.8 will handle anything you can tow with an F-150 anyway.
Basically you can't go wrong with either, but if you need the extra power opt for the 5.4l.