Here's a picture of the trouble spot. It's enlarged from the CLC Eastport pram gallery, hence the less than perfect quality (not that there's anything wrong with the gallery. The image quality is causd by the fact that no one really has a good photo of that area and I had to extract it from the one photo that came close and over-enlarge it to show the problem spot).

We can see the forward seat with the hole for the mast. Directly under the seat is the mast step. Surrounding the hole on the underside of the seat is the mast step. We can see the edge of the mast step as it passes in front of the white inspection plate. The inspection plate is mounted on the forward bulkhead. The seat rests on top of the bulkhead, forming a watertight box. That introduces the cast of characters.
The problem, if I understand it correctly, is that the forward bulkhead is too far back so that instead of passing in front of the mast hole it passes under it. This is a problem because the mast won't fit. The bulkhead can be forced to bend forward clearing the mast hole, but the mast partner still won't fit. It sticks out the back of the seat.
It sounds indeed as if the boat is not quite put together as designed. The problem is that at this point in the build, the forward bulkhead is immovable, having been glued in place.

So my first question is - have you glued the seat in yet? Second - when you hold the mast partner in place, how much does it stick out towards the back?
As far as fixes go, they depend on the answers to those questions, but here are some possibilities:
1. If the seat is not glued in yet, move it back until the mast partner fits. If the gap is small, say 1/4" or less, fill the gap with extra epoxy/woodflour putty. If it's larger, fill it with thin strips of wood and cover with epoxy/woodflour putty. For extra strength, cover the fillets with fiberglass tape.
2. If the seat is glued in, flex the bulkhead forward until the mast hole is cleared and glue it all together. Then, glue the mast step to the top of the seat. If you row with a passenger sitting there, give them a cushion to cover the bump.
Do not reduce the size of the mast partner and do not add shrouds. A boat has to be specifically designed for shrouds with the hull reinforced to handle the forces transmitted from the mast to the hull. This pram is not.
Anyway, post some pictures showing your exact situation and answer the 2 questions if you want a better answer. The good news is that this is fixable and you're going to have a really fun boat.
Laszlo