As to the 550a limit, Kelly advertises their controllers using the phase current. Your controller may put out near 550a phase current when the current limiting is not in effect. The phase current is not measured by the cycle analyst, only battery current. You could put a clamp meter around a phase lead to determine the phase current. It would be impractical, but not impossible. There are also higher current Kelly controllers available. I have seen motorcycle builds with higher amp kelly controllers.
It is somewhat shady advertising to label the controllers that way, but the spec sheets do define phase and battery current limits.
There is at least a 1000a maximum phase current kelly controller, I think there is also a higher current 1200 phase amp burst controller.
Here is the 1000 phase amp controller:
http://kellycontroller.com/khb1210124-120v1000aopto-bldc-controllerwith-regen-p-738.html
It may suffer from the same low speed start current limiting, though, even if it does, the limit would probably be higher than the 550 phase amp controller you have.