Further invoice customization is planned as a feature in a later release, but current priority is bug squashing so that maybe awhile before it's implemented.
3. Ability to display custom invoice numbers. I changed the invoice number format to [PREFIX][YEAR]-[NUMBER:0001:RESTART:YEARLY] but when I display [INVOICENUMBER] I get the default 16 digit invoice number.
Did you change the format after the invoice was already created? Please note invoice numbers are generated and stored. Changing the format after an invoice is stored does nothing to existing invoices.