<p>I have a z-axis which follows schematically the same principle as the makerbot one's (threaded rod and two leading rods with linear ball bearings carrying a level). It is from an old experimental lab doing physics or chemistry.</p>

<p>The axis move gorgeously about 5 cm, but then it get's stuck on either sides of this way. Both driving threaded rod and the leading rods seem perfectly fine and should be able to allow for further movement. This is as far as I can see by eye.</p>

<p>Where should I look to find further issues and how could I improve the performance? Do I need to take the construction apart?</p>

There could be a few issues at play.
The smooth rods are not parallel which is causing the bearings to bind the further you go up.
Part of the thread is damaged not allowing it to pass through the nut.
The threaded rod is bent significantly to where it either doesn't pass through the nut or bind the assembly. (Is the end of the threaded rod opposite the motor constrained?)
Even less likely is that the motor could be damaged.  Since you said it moved 5mm I would have to assume that is several revolutions of the motor so this is unlikely but possible.
The easiest way to find the problem would be to unhook/remove the threaded rod and see if you can move the carriage up and down the rods by hand, if so you just narrowed the problem down significantly.