Which one is better? (long)

Why would you need to cut the floor for an a727 which most of them came with ? The 904 is not an o/d trans.
Make sure that the tank is supposed to be vented. Most factory FI cars will throw a code if the gas cap is loose. That indicates a non vented system.
Also if using a factory ecu you may have to add various sensors to your engine as well as O2 sensors.

Are you trying to use all the factory stuff to make it look like it is stock or trying to save a few $ ?
You might be a little unhappy with the performance of a totaly stock setup as the 5.9 was only available in trucks and as such is not a performance setup.
Aftermarket FI systems are much more user friendly and can be tuned. The factory setup really can't.
I might rethink this before you start to buy things.