It doesn't matter how many applications you have installed from extras-devel. Even one may brick your phone if you are unlucky. extras-testing can also do the same though less potentially.
1)[...]You didn't say what MSN are you using. If you're using pidgin, there I can confirm you that its problem isn't related to N900 in any way. I encountered lots of problems with it I don't wanna whine at, I switch back to telepathy-pecan which is stable and great. 2) Regarding contacts problem with telepathy-pecan, first you must check whether you've flashed your eMMC when you flashed your ROM. You know, when they said there's new eMMC format with new ROM they definitely MEAN it. 3) You must know Joikuspot has some minor issue with your overclocked kernel, and even I'm not surprised to see it has other problems with stock kernel as well. Try mobilehotspot if you wanna build a wifi hotspot. I wrote my own script to make my N900 a wifi hotspot for greater flexibility and power-saving. If you'd like to try I can share with you.
I develop on the phone, so I tend to play around with things quite a bit. But I've never rendered it unusable. You should always be aware of what you're actually doing entails. Anything that messes with the Kernel, over-clocking or whatever, if you're just a "normal" user, it's a bad idea.
In myopinion: You either have faulty hardware resulting to these issues. Or you're doing something wrong. I never had any of these issues, and I flashed countless times because I like to mess with it.