1. The base reference indicator is not a UEB symbol and will be longer be used. Follow print for whatever symbol is used to indicate a footnote (superscripted numbers, daggers, asterisks, etc).
2. The BANA Formats Committee is recommending that the 7th transcriber-defined symbol indicator be used (dots 46, 3456, 1456) to indicate that a note is present. This is not yet approved by BANA. In the case you have sent, if all the highlighted words have footnotes, a transcriber's note could be inserted on the TN page stating that all the highlighted words have related footnotes which can be found at the bottom of the print page. The format for the notes themselves has not changed with UEB. You would then not need any other type of indicator. The highlighting should be shown using transcriber-defined typeform indciators (which would need to be shown on the Special Symbols page).
I am not certain I answered all your questions. If I missed something, please let me know.