Can't access categories after Magazine Basic Update

Hi I recently updated wordpress and magazine basic on http://cyclistsinternational.com, and of course didn’t read the fine print, so I lost a lot of my formatting. Though much of the content is still there.
After spending some time on it, I did encounter some critical issues, however;
(1)
I had set up a long list of categories in hierarchy, that are reflected in the top nav bar.
However, now when I write a story I don’t have access to them any more–the dialog box won’t move down through the menu choices. I can’t do it there or on the dashboard. Big problem, nothing is being categorized properly any more.
(2)
I can’t seem to access my dashboard. The sign in used to appear on the upper right hand corner. No more. I can’t find any back doors in either. So I can’t change my site–at all.
(3)
I lost all the special programming my programmer did to accommodate my own ads. I guess I will have to rewrite these from scratch? they were created as stories and slotted into special spots. Unless someone here can recommend a good advertising widget, I never was able to find one that I could understand.
(4)
I don’t like the new fonts in some instances, and in others the spacing is off, so words are being slammed to the edge in some of the widget boxes. Is there a way around this?
(5)
Other changes I do like however, so this is not really complaining, just adjusting…
Help!
Jen B