The font embedding can be a problem if not done and you are trying to view the PDF and do not have the font on your machine. Acrobat will often try to find a replacement, but it is not always a good choice. Sometimes the "Use Local Fonts" button can be changed in state to resolve some of the viewing issues.
If you are trying to copy or export info, then it is important that you have the fonts on your system. Otherwise, the message you are getting about embedded fonts would not be showing up.
As for Excel formatting, be sure that the Adobe PDF printer is selected in the printer screen before you look for the paging and formatting of the file. In most OFFICE programs, if you change the printer the application will reflow the document to best match the printer (called "using printer metrics"). So check before you create the PDF that the layout is correct.