Dear Ken,
You're right, you have to have an active imagination to complete this task!
I cut
both the cabin moulding and the flying bridge moulding to get them to fit together, but be warned, I couldn't find a good fit. I'm not sure they do match up together properly. I ended up cutting too much away from the cabin roof, but after liberal application of P38 all was well.
First you need to do a trial fit of the perspex inner walls to the cockpit (instruction .pdf, page 6, sheet B, 1.5mm perspex, part of item 31) to determine how far
back to set the upper helm moulding, and also the same with the floor of the flying bridge to determine the cut-off point between the floor and the bulkhead with the door in it (This floor sub-assembly is on the same sheet of perspex, again items 31- stowage wall- , with the upright parts for the liferaft stowage on page 10, sheet C, 3mm perspex). Does that make any sense?
Here are a couple of photos to show where my joins ended up.


In the lower photo, you need to make a solid join between these two (where the red line is) inside the cabin. I superglued them together first, and then used resin and glass tape to make a solid join. It's not going to show later. If you need more info, let me know and I will get a photo before it all disappears under primer.
Good luck!
Chris