The install is finally done, and car is running great!! Couple of recommendations based on my install experience:
1) Reinstalling the back manifold bolts can be a pain, especially trying to get a torque wrench on them! I would set the intake manifold back on with the bolts sitting through the holes already so you are not trying to get a magnet back there to get them started.
2) Keep the heater core hoses disconencted till the very end, definitly helps to move those hoses out of the way
3) Replace and grease those heater hose O-rings, suckers leaked on me twice after the isntall was done.
4) Double check cylinder #3 coil connector, hard to get lined up and hooked on, it fell off on me, cause a miss, but the engine Code led me to the fix on it.
5) Spray the EGR tube with lots of wd-40, sucker was not happy coming off at first
6) make sure the rubber grommet for the shifter cable is isntalled right, I noticed mine was out a bit and it was hitting the EGR tube and melting!
7) Replace all the spark plugs with the manifold out, MUCH easier to do this way, but before pulling the plugs, spary some air down in the recess where they sit, the fluid can build up in there and when you pull the plug it drops in the motor.
Finally, definitly be careful with those 5.4 manifolds, they are 1000 bucks from the dealer and very scarce on eBay, be gentle