Alright, I see I have to spell this out for you.
The 2.9 was always a V-belt engine.
The 4.0 was always a serp belt engine.
On a V-belt setup the water pump, and all other accessories spin in the same direction as the crank. This means the fan clutch needs left-handed threads to not work itself loose just because the engine gets started.
On a serp belt system some accessories spin the same direction as the crank, some go the opposite direction. It depends on which side of the belt they are on. On the 4.0 the water pump pulley is smooth, which means reverse rotation, so that allows for use of normal right handed threads on the fan clutch.
So the difference in the type of belt used means that even though the bolt spacing and hole size on the pulley may be correct (and probably is) the pullies don't interchange because the belt surface isn't even close to correct.
Now on top of all that, your question about the pullies is moot anyway because the fan clutches on the 2.9 and 4.0 don't bolt on top of the pulley like the 2.3 and 5.0, but rather they thread on to the snout of the water pump.
And no, before you ask that question, and I know you will, you can't just slap a 4.0 water pump on a 2.9 and make this work either. Because they spin in different direction the fins on the impeller are pointing different directions. A 4.0 water pump would spin backwards and create almost no flow.