This is a lot in one post. You might have to re-ask some of your questions and you might have to supply pictures to explain better.
1) very hot motors is normal
2) You need to show picture, sorry.
3) Go to the tune menu. Once you hit "print" you can immediately go to tune and change settings before it actually starts printing. After you exit tune menu it will start printing if up to temp. While printing you can go to tune menu and mess with other settings live (such as retraction distance! couldn't do that on a UM original!).
4) Water works fine. I usually use glass cleaner and a rag as glass cleaner evaporates faster.
5) If machine has been hot for a while I usually manually extrude before I start the print. It's buried in advance menus somewhere. "move material" maybe?
The temperature setting is totally handled on the printer now, so that it's removed from the Cura. Similarly, the filament diameter, and retraction speed and distance are set in the printer, not in Cura.
One thing to check... Is the 3rd fan on the back of your print head running all the time? It should come in as soon as you turn the printer on. Some folks had problems with the wiring of those out of the box, and that can cause print quality problems.
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