position and size of footnote numbers

I don't believe there's any way to adjust that, since the size of the superscript is based on font size at the insertion point. There's also no way I know of to change its location in a line of text, since it just uses the standard superscript.

What you can do, especially if you have a lot of footnotes, is increase the line space for your paragraph tags to 1.5 from 1 (Single). That should provide enough room for the superscript to be inserted without leaving a weird gap in the spacing for one line in a paragraph. If it doesn't, or it's too much room, adjust the spacing by .1 increments.

Edited to add: You could also try applying a character tag to the footnote superscript after it's inserted; however, that will only adjust the size of the text. There's no way through the FM interface to adjust baseline locations that I'm aware of, and I don't believe there's a way to do it in the MIF, either, but I could be wrong.