Marc, gaining the full travel from the mechanism requires everything to be adjusted just right. It is almost CERTAINLY not a function of the motor assembly, but the geometry of the mechanism upon which the motor acts.
This picture shows most of the mechanism. If the geometry is wrongly set you will easily loose the total travel.
What I would check is that:
1) the length of the lever against which the motor pushes is correct.
2) That the distance from the pivot point to the attachment of the screwed rod is correct.(You have the crucial dwg that defines this? If not perhaps I can find, photo and send. If the builder made it wrong it should not be too hard to make up a new lever arm.)
3) That the angle of the lever at full retract and full deploy is equal. If it is not you will loose travel.
Once you have those set correctly you need to make sure that at the limit of the retraction the flaps are indeed fully up, but no more, by adjusting the pushrods that come through the wall of the fuse. Once that is all correct I think you should find you have the full travel that VANS requires, or even a couple of degrees extra. I suspect the extra degrees are lost under air load.
I spent a long time on this because stopping is very important to me because of the
length of my strip.
If that is less than clear, just ask.