Footnote numbers and periods

To line up the periods, you will need to add a tab in front of the footnote numbers. You can add that tab in Footnote options as a prefix, and then set the tab stops in the Paragraph Designer. This post addresses this topic for numbered lists, but once you know how to add the leading tab to footnote numbers, it works the same way.

Adobe FrameMaker: Aligning Punctuation in Numbered Lists - Rocky Mountain Training

If the footnote text is getting shoved, it sounds like you just need to adjust the Alignment:Left and first Tab Stop for Paragraph Format Footnote.

If you are trying to get vertical radix alignment for the period, I'm not aware of any trivially obvious solution. I can think of a hack, built on the suggested method of doing Endnotes, but in tables within column-bottom anchored frames, but if you are already into to 3-digit footnotes, managing large number of AFs, each with different height, might be far to much trouble.