are you using a LVC or a monitor of some kind like the celllog 8 ? If not, I wouldn't take it below 36v . I don't remember if you said you were using one or not. If you get a monitor, you can use a lot more of the battery.

Did you end up getting a 35 amp controller? That's what I have too. Do you know what the max amp peak is on that? Max amp peak on mine is 43 amps. The cycle analyst should tell you what it was at the end of the run. The Thundersky do fine with anything up to 2C which is about 40 amps.