I am using Milestone 2 for some months now, and I think I can tell my experience for some of your problems (though they may not be much helpful, sorry for that).
1. The battery problem. I think I had such issue once, and I solved it by just leaving the MS2 charging for the whole night, despite the indicator showing 100%. I think it may sometimes show 100% when the battery is far below 100%, that's why it drops rapidly to 1% when the meter realizes the truth
. Recently I have also had the opposite: The phone discharged to 1% (in cold and humid conditions, that may be the cause) and I switched it off. About two hours later, when it got the normal temperature, I plugged it to the charger to see the battery indicator at... 60%
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2. The (tele)phony problem
. I had some dreadful ordeals with this problem. It started about one month after installing CM (don't remember which version that was) - the telephony layer crashed often when I was in one specific area of my city. Then It slowly started to crash in other areas, and finally was crashing about twice a day (sometimes twice in a minute) everywhere. (due to that, I think the problem is somewhat related to the moment when the phone switches between GSM antennas). I tried quite many things, including installing cm10 by czechop, cm10 and 11 by Engle_Mars, reverting to stock (un-rooted) and rooting again from scratch, not installing any apps. The only time it was not crashing was when I had stock Gingerbread installed. (Interestingly, even with vulnerable roms it never crashed during a call). I tried also increasing the processor voltage values (OPP), and lowering the max frequency, but it didn't help either. Then I went for two weeks to my parents for Christmas. My parents live in a village, where there is only one antenna, and... the phone didn't crash at all through that time. But what was even more strange, when I returned to my town, the crashes did not return (and it's been 4 months since). Now I don't know what to think about it, but... if you can, try going to a village for two weeks, maybe that helps
. The crashes did not return, but recently the phone reboots occasionally (usually after ending a call), but that's once per two weeks, so it's not very inconvenient.