but really very little clue about using the ISP interface
Start by using AVRDUDE from the command-line to read various things. For example, this...
avrdude -v -v -v -pm328 -cavrispv2 -P\.\COM8
...attempts to communicate with an ATmega328, using the "avrispv2" protocol, through a programmer at serial port 8. The command is always safe to use; it only performs reads.
Once you have that working, try reading the program stored in Flash. Try reading the EEPROM. Try reading the signature bytes. Basically, ensure that AVRDUDE is working correctly.
At this point you will have a way to manipulate the processor any way you wish. There are only two things that you need to always ensure... setting the "Serial program downloading (SPI) enabled; [SPIEN=0]" fuse and not setting the "Reset Disabled (Enable PC6 as i/o pin); [RSTDISBL=0]" fuse. (Almost) everything else can be undone.
To install the new bootloader, the processor is "unlocked" (some fuses changed), the bootloader is uploaded, and the processor is "locked". I suggest doing this by hand (AVRDUDE from the command-line) a few times to ensure you have everything the way you want. After making a few changes to boards.txt, you will be able to install the new bootloader from the Arduino IDE.