Yes indeed. Pretty much any small block Ford bellhousing that attaches with six bolts will bolt up to any other. Some 1966 and older 289's and 260's used five bolt. THOSE do not swap with the later six bolt ones.
A very similar set of circumstances there for sure. With one big giant exception. 1986 5.0 are reknowned for having the "worst" stock small block regular production Fords heads and the GT40P's are regarded as the best. Polar opposites.