"I have analysed it as a pinned base portal frame, but the moment connections in the timber don't work (no surprise there)."
You are going to get some fixity (and moment transfer) in your bases there.
I have used fastrak and portal frame extensively. I can answer any specific questions you may have.
I feel the portal frame software is very good - the building designer software is good if you do a lot of scheme design with steel (it only does steel). Its good for stability and floor...