Yes, the 4.0 is to a 2.9 as a 351windsor is to a 302.
The Deckheight is raised 20mm.
So, no the heads/manifolds won't work.
The Exhaust manifolds would bolt right up but then your Y-pipe would no longer fit.
The 4.0 with it's higher deck uses exhaust manifolds that "hug"
the block a little tighter so that BOTH the 2.9 and 4.0 bolt up
to the same Y-pipes...
I believe ford played the same trick on some F-series trucks with the 302 and 351
This information is "useful" because in something OTHER than an F-150
using 351 manifolds can make a 302 fit easier into a tight engine bay.
AD