Been there myself, Guy.
You and your father seem to have gotten along way better then mine and I ever did - but a dad is a dad and only time will heal the pain thoroughly, if not completely.
Building models was one of the few things my dad and I ever did together.
I can still remember him first taking me to an old local model shop when I was about seven years old, and I treasure my memories of going there with him through my childhood.
It's a great thing that you were able to share your love of Star Trek and he his hobby of modeling.
I'd be willing to bet that many many sci-fi modelers have similar stories of dads who got them started in model building, so really I think this thread is very appropriately placed.
When I was a kid I modeled out of imagination of the future. As an adult, I mostly model out of nostalgia and because it helps me enjoy the memories of my past.
If you don't still have one of each of those old AMT models, go ahead and treat yourself when you can and keep them somewhere prominent in your home.
As long as you have your memories of him, your dad will never truly be gone.