Question 1) - Quote from datasheet: "The MCP7940N features two independent alarms.
Each alarm can be used to either generate an interrupt
at a specific time in the future, or to generate a periodic
interrupt every minute, hour, day, day of week, or
month."
So, yes. You can do this. Set the Alarm for 9PM. When it occurs, enable the Interrupt for every five minutes. Every five minutes, once you do whatever you want to do, check the time. If it is 5AM or later, disable the Interrupt for every five minutes.
Question 2) - Actually most of the Pins can be set up to Trigger an Interrupt. The Pins which are specifically for this purpose (Pins 4 and 5 on the chip, designated as D2 and D3) are just easier to use that some of the others. However you go, you can always poll to find out WHICH pin caused the Interrupt.
Changing the times from 9PM or 7PM or 2AM to 5AM is simply in the coding. If you hard code them, you can always Change the program. If you try to use some type of configuration the bigger question is how to Change the configuration (menu driven, several pushbuttons, read from SD Card, etc. The sky is the Limit)