How I do it is put it into service position and take the clamshell off (6 bolts underneath) so you can get to the rods when it's closed.
Start with the plastic ball joints screwed on as far as they will go. Close the top most of the way, stop and loosen of the bolt on the push rods on both sides, let the top slip as far forward as it wants to go till it's resting on the window frame, but don't latch it up, then run the motor all the way closed. Then pull on the b-pillar pieces ever so slightly to get a tiny amount of slack between the frame front and the window frame, and tighten the bolts back up (if you run out of room on the bolt runners, then you can turn the plastic ball joints a few times to get more length).
Carefully run the roof all the way back, then all the way forward again, and watch how the front moves when it gets near the window. If you give the rods too much length, the top will reach the window slightly before then end of the run and kind of 'bounce' and retract back again (this places stress on the plastic joints I think, which may be what you had when you fitted it latched). If they are too short, it will come up short of the window frame (and you'll need to pull hard on the handle to latch it, which will stress the top and it'll eventually separate at the back... see my recent howto fix that
). If either happens, loosen of the bolts and try again. You want it so it just gently touches the window frame, or even a few millimetres before.
When you think it's good, run it back and forward a few times to check nothing pops, then bolt back the clamshell and give it a try....