So purchased a 2000 Dakota 4x4 160k 3.9L V6 AT. Check engine light, scanner showed Cyl 5 misfire. Engine not coming up to temp. Went in to replace thermostat as the original was stuck open. Cleared codes and ran drive cycle, noted rough idle after drive cycle engine still not at temp fully, cyl 5 misfire shown.
Replaced plugs, wiring, cap, rotor, still cyl 5 misfire
Replaced #5 injector, after warmup cyl 5 misfire, although it did idle smoother.
Next step compression check all above 160 except first run on 2 was at 130 second run came up to 150, cyl 3 was at 190 initially, 175 second run.
Replaced lifters, cleared codes, after drive cycle, cyl 5 misfire. Noted oil residue on #5 intake. No indication on plugs.
Replaced Crank position sensor rechecked drive cycle, again cyl 5 misfire.
OK let's look at the top end. Pulled heads to see what was what. Drivers side cracked between intake and exhaust seats on cylinders 1 and 5, noted no wear ring on #5 exhaust valve as if it had never touched the seat, and a large buildup of gunk on the stem that prevented it from seating fully, Valve springs etc. were all good. . Same on passenger side 2 and 4. Purchased a set of rebuild heads, noted welding repair on the journals between intake and exhaust on cylinders 1 and 5 and also on 2 and 4, since the heads are mirror images this was expected. Put the heads on, cleared codes operated drive cycle all code and sensors came up normal. Engine came up to 180, O2 and Evap sensors cleared.
Noted the meat in the casting between intake and exhaust on the outer cylinders was about 1/16 less thick then the center cylinder. Looks like this may be a common failure mode on the 3.9 liter Magnum V6.