Two words : Predator Warranty.
If you are the original owner, the shaft is guaranteed for life.
Meaning, Predator would replace your ferrule for free.
You just pay s/h.
They don't have to guess at dimensions. They've done a few already.
The reason that I've returned to inform you of this is because that,
the more questions that you ask, the more you reveal of your knowledge/experience with the subject.
Unfortunately, knowledge & experience aren't included in the "Cue Companion" pkg.
You speak of wanting to keep it original. Predator already knows how to do that.
You asked : "Do I leave a gap between the top of the stick/tenon and the cap or should it be flush?"
My response will be in the form of a question that I'll leave you with to think about for a while.
Do you want the underside of the ferrule cap to be your initial contact point to the shaft
or do you want the ferrule's bottom edge to set on the shoulder of the shaft ? It can't be both.
Again, Predator already knows.
Let's consider further, ie, that you're not the orig. owner and that you have no warranty.
Predator has the correct ferrules in stock, they use the correct epoxy and they know what they're doing.
You on the other hand, have a Cue Companion and no instructions. I'm told that I'm harsh but am I wrong ?
Call Predator Warranty about cost. I'm sure that you'll find it to be very reasonable.