3.5's, 3.9's & 4.3's have the short nose crank but their journals are small (2.0in/50.8mm big end & 2.3in/58.4mm main) unlike the 4.0 & 4.6 which have large journals (2.185in/55.5mm big end & 2.5in/63.5mm main) so a 4.0L crank won't fit a 3.9 block without machining it down. the 4.0L & 4.6 also have long nose cranks hence why the 3.9L crank won't reach the front pulley when using your 4.0L cover etc.
My 3.9 is a late interim block with a 10 bolt head and the p38A block but it is not drilled for the X-bolts (but can be drilled and tapped)