It still could be cable adjustment. I blocked mine between the struts that hold it when it is down and the bottom ledge of the upper half. If I remember correctly the 2x4 blocks were 27" long which allowed the top to lower several inches below max height. Then adjusted the lose cable(s) to the same tension as the others. This only got me to within 3/4 of an inch. From there I just had to adjust and check the measurements. I could not distinguish any differnce in tension. A six inch difference could certainly be causing the upper half to bind.
Are the cables on all of the pulley wheels? Pulley wheels good, the cables havent cut through. Did the cables get caught on something on the frame while not under tension during the guide replacement.
Another cause could be something that has gotten in between the two halves and is jamming but this would only be the cause of it not going all the way up.
Is the cylinder extending fully?
If you didn't have these problems before the guide replacement, check your work. Sometimes a little break, hours to days, clears the mind, lessens the frustration level and the problem suddenly reveals itself.
Just a couple of things that come to mind.