Well,
first I have to say that I am a newbye on HFSS. I am curious about your waveport definition, what was wrong with it?
On the BPF, HFSS is not the right tool to design it. Or, better, it is not a good idea to begin from it. I would start from a circuit simulation, using ADS or Designer, where you can tune the parameters without re-frawing everything. Then you generate the layout, and you do the fine-tuning using a planar simulator. You can then verify the results using HFSS to take into account the fringing effects and so on. If you start from HFSS you simply will have too many degrees of freedom.