We need to see pics of a 5.3's passenger side manifold's 3-bolt flange face plate.
I would think with all the folks here swaping motors and doing header installs, one of you would have one on the old 5.3 or garage floor.
If not a pic, please discribe rather or not, or how it differs from the drivers side.

 

Here are some that should help.

#1 Drivers side manifold (on left) and passenger side manifold. That is no illusion, they have different bolt patterns. The pass side uses the donut gasket (insert).

#2 Driver's side Y-pipe flange

#3 Pass side Y-pipe flange. Notice the flare for use with the donut gasket.

Hope this helps you out - I didn't know about these differences until I took the pictures.

 

Snake is right, the big difference is the donut use on the passenger side ONLY.
Sorry, no pics just the header and engine swap.