1) Sorry, I'm not willing to work this out for you. The Custom Design upgrade is supposed to come with staff support, so if you wish you can wait for a staff reply. You may have to wait long. Roughly I'd say that to do what you're trying to do I'd simply make #contents and #widgets float left. But you need to change several widths and other details to make this work well.
2) And actually I agree with raincoaster, first because changing fonts, colors etc is easier than rearranging sections, second because I don't see what's so special about Chunk. What exactly do you really like in it?
3) Themes with a right sidebar listed here (under "One sidebar", "Two or three sidebars", "Sidebar(s) plus bottom and/or header"):
(Newest themes not listed - check the red note in my sidebar).
When you say you previewed other themes and the widgets were at the footer, do you mean themes with a right sidebar? If so, then the preview was affected by the CSS changes you have made. Also, when you preview a theme with a sidebar, it will display its default sidebar items: it cannot display the actual widgets you've added to Chunk. So if you wish to try other themes, better temporarily remove the CSS you've added and activate the themes instead of previewing them. Or see the themes in action here: