Thanks for the insight of Your procedure.
I myself have little experience with AWR microwave office and process is quite similar. First, built in tool (called iFilter) generates perfect model based circuit, then it can be exported to AWR and simulated using AWR models (it takes in to account cross-coupling, vias, etc). I usually optimize the filter at this stage with built in optimizer (usually for particular return loss). Then filter can be simulated and optimized with one of AWRs EM simulators, like Axiem. I never tried more than ~2 GHz, but usually I need to trim resonators of actual filter, because pas band usually turns out little low, even with all the EM sim. which includes vias and enclosure.
You mentioned milling - from experience with such process, milling takes off a little bit of material also, not just copper. Does it affects the results of filter, knowing that coupled edge region is very critical for these kind of filters ?