The head is the real downside on the late model... they don't all crack, but bad maintenance and abuse will make it more likely.
The axles suck somewhat on the late models too, but if you're lifting it, you are only a few bolts from swapping them anyways. The d35 is trash and the lp30 isn't quite as good as the hp30. If you don't mind dumping the ABS you can throw an 8.25 in the late model easily, you will need new U-bolts but they will probably come with the lift kit anyways and should be replaced either way. The transfer case output shaft setup on the late model 231 is more prone to vibrations but that's a moot point if you plan on installing an SYE anyways. IIRC, a 4.0/aw4/231 with SYE/8.25 drivetrain is about the right length to run a regular 4.0/auto front driveshaft as a rear driveshaft, which negates the need for a custom shaft or finding a replacement to fit a late model with an 8.25 when you swap the 8.25 in.
It's really up to you, there really aren't many problems with the late models offroad with regards to body/electronics.
