I can't answer on all of them but I'll do what I can ..
1. If you want a customizable chat window on the right that keeps its settings my Chat plugin should do that for you .. Whispers and Guild will always default to just displaying guild and whisper only messages. I am still seeing some glitches with how the chat window is created but I believe I have made a note somewhere either on the addon page or on one of the threads about it to work around the glitch until I can figure out why it happens. As to the combat log, I would assume that nUI keeps whatever settings the combat log has had done to it but Scott should be able to confirm that himself.
2. Hmm, don't recall if I've seen this at all or just ignored it assuming its something I've done but will try and look out for it myself.
3. I usually have my UI scale set to the minimum of 60% I believe and then I reload the UI to make sure it resets. The game doesn't do it properly if at all automatically and you have to do it yourself.
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