Thanks for all the tips you guys. I decided to take a break from the modeling side and decided to try to get my ship to work in FS, first time. It was a success, even the test mission works, kinda:

but the beams fire!

After a quick investigation I found out why the ship decided to dock upside down, the container's dock point is underneath! :doh:
Also the nose passes thrugh the container while approaching to dock, but I fixed that by extending the container's dock path. Il keep this in mind when I start to POF the beam module.
If your wondering, the Fenris beats the Jaseyd if it gets if main beam to bear, otherwise the Jaseyd pecks it to death with its AAFs.