Some interesting points.
You are getting good performance and you are obviously running clear of stall, this is the best way to get good power but I think your 1200W is on the high side for long term survival. Much depends on where your losses are occurring, if it is all in the stator then it won't last long. If it is mainly in the connecting leads then things are much better but even so I think you are pushing the stator rather hard.
The fact that it won't stop with a brake switch is a sure sign that you have low overall efficiency somewhere, these machines seem normally to run well stalled and will stop with a brake switch. It may be that you have a very wide air gap and are running faster than normal or it may be that you have a lot of line resistance, both of these improve the high wind performance but mean that you can't brake it in a high wind.
You were right to leave it run, if you hadn't it would have burnt out, the power dissipated in the stator would be near double when shorted. You can only consider your shorting switch as a parking brake for erection.
It would be interesting to see what volts you get at the base of the tower compared with at the battery to see what sort of line resistance you have. It may be that the brake would work right at the base of the tower.
There is something to be said for the argument that windmills should run in all wind conditions, it's bad enough that they don't work in low wind. On a good site clear of turbulence this may be a reality but on my useless sites things get very challenging in high winds and I prefer to be able to shut the things down. I always use another shut down method, I have never relied on brake switches because they don't work if you have an electrical fault, but for normal operation they are ok AS LONG AS YOU CAN NEVER BREAK AWAY FROM STALL.
You are lucky, you found this out very early and took precautions. Many don't find this out for a long time and then the very high wind comes and it breaks away and burns out. Similarly you know where your furling point is, some running very stalled assume they are furling when it is in fact stall regulated and one day the big wind comes, it pulls through stall and furls at a speed far too high to protect the winding.
I am pleased you have got things working nicely but if it was mine I think I would try to get it to furl earlier for peace of mind, there is a lot of increase in stator heating from 800 to 1200W. Whether it survives or not depends a lot on the duty cycle, if you only get 1200W for a few seconds and then a long interval of less power it gets time to cool, but if the wind conditions get to such that it is near continuous at 1200W then the heat doesn't get away. I know that on bench tests this power can't be sustained but none of us really know what cooling there is in a 40mph wind, it is obviously significant but I suspect it's not as much as you would think.
Flux