I resigned the entire ROM (except google apps) when doing Tsugi, so I may have avoided signature problems that way.
As far as Wifi, mine has settled down and is working well, though it has gotten "stuck" on an old wifi once this week. That's a problem I see on my TouchPad as well, so it may have to do with the Apple router at a friend's house which is the network they tend to get stuck on... the device will think it's still connected even when you're miles away, and of course, it isn't actually connected. Have to toggle wifi off and back on.
Are you still using older versions of aapt/apktool/baksmali? Or have you updated to the latest versions? That could be an issue, might try switching versions to older and/or newer.