Well, I seem to have figured out my own problem. I'll post about it for the benefit of others who may attempt this mod.
1. I charged up the 72V (20S) battery to full (84V) - not sure if this matters at all.
2. I plugged in the 52V battery to the Phaserunner (I originally configured with this battery), launched the Phaserunner software, and plugged in the USB.
3. I followed the instructions on ebikes.ca to reflash the "Default Parameter File."
4. I disconnected the 52v battery and plugged in the fully charged 84V battery.
5. I entered the approximate kv of the BBSHD (70 RPM/V) and pole-pair count (4) in the software.
6. I ran the autotune test (spun backwards on first run).
7. Leaving the battery rated voltage at 48V, I changed only the regen voltage (BBSHD can't regen anway), max power and max current settings.
The bike now runs fairly well on 72V limited to 3000W. I ramped the acceleration from a stop to be slower using CA3 throttle ramp (1V/sec up). My only remaining issue is that I experience a motor judder whenever I coast on no throttle and reapply throttle, such as coming out of rolling through a corner or coasting down a hill. I've read that this is not exactly easy to fix, and that a minimum throttle output setting might be one solution.
Can anyone point me in the direction of useful material for fixing/reducing this judder issue? If I solve this, the bike will be basically perfect. Light, stealth (except for speed), silent, powerful.