1) When I hover over a particular map point in StatPlanet, it will not highlight/show the data for that particular community (and I have made sure there is data for the indicator/year). Any thoughts of what I might need to tweak in the "settings" tab of the Data Editor file?
2) I mentioned needing to remove two communities (that are within the shape file) from the region drop-down menu. In the "Map regions" I have removed the Start (ISO) codes, but that only removes those communities from the particular region from which they are associated? Can I remove them from "Import" and the "Data" sheet? Or does everything have to be done with the "Map Regions" sheet?
Sure you can also remove regions from the import and data sheets. Besides these two, you would also need to remove it from the 'import names' sheet, otherwise the columns will be mis-aligned after importing data. Removing regions yourself can cause issues where the columns not match up - so if you do encounter unusual issues if data/names displaced you could see if there is an issue here (as described previously).
For map points, it can be useful to create a 'dummy' category/indicator with just one year, with dummy / fake data for all map points. This is just to display every single map point. A new map point normally appears in the top left corner. If it's not there, it should at least be listed in the list of map region in the 'selection panel' in the top right corner.