I believe the SYE was first made to accomidate the 6" coil spring lifts for YJ's that were made by procomp and black diamond (warn) a while back (1996?)
Since then, they have been recomended for 4" lifts so there is no need for a T-case drop. I have 4.75" of suspension lift with axle shims. In the year that I had this lift with the original driveshaft, I when through 4 U-joints, and 2 pinion yokes. I went with the Advanced adapter SYE and Tom Woods (very popular selection) I have had no problems, in fact, I have less deceleration vibration, almost no vibration during heavy acceleration, and a lot more confidence in my U-Joints. Plus the output shaft is a lot larger and beefier, and this allows for future mods such as a belly up skid plate, a SOA lift.
The reason why some people have issues with slip yokes, and lift kits and some people don't. (I heard this straight from Tom Woods' Mouth) When Jeep manufactured YJ's, and early TJ's, Particularly 93-98, there is some discretion in the measurements of the drivetrain. When I first went to install my Tom Woods drive shaft for 4" lift it was about 3 inches too long.
It was the correct part, but for some reason my entire drivetrain was set further back than some other applications. The drive shaft I ended up using is for a stock ride height (even though I have 4 3/4" of lift). This was also the cause for all my previous U-Joint issues. Due to my drivetrains position, the angle of the U-joint attached to the pinion yoke was very drastic, hence destroying U-joints.
The story Junkpile described sounds like he had the oposite problem, his drivetrain was set further foward. Hence the slip yoke was pulling too far out.
As for the Fork and Chain thing. The New process 231 (most jeeps after 87 are equipt with this) are chain driven as opposed to the gear driven units found in many CJ's. The fork is what physically pushes the gear onto the front output shaft in-order to activate the 4wd. and the chain connects the two gears, one on the rear output shaft and one on the front output shaft.
And yes the instruction could have been better!