Checklist on getting the N64 MisterFPGA core running (after searching a lot in the forums, myself)
Delete any .cfg files.
Make sure that you have the latest version of the core.
Make sure that you have the latest version of N64-database.txt.
Make sure that you have the N64 BIOS. You can get the BIOS from the MAME 0.260 non-merged ROMset. The BIOS is the .bin file in the .zip file of your choice.
Rename your choice of BIOS to boot.rom. (Remember to change the extension, not just the name.) Any additional BIOS would be renamed boot1.rom and boot2.rom if included.
Put the BIOS where the N64 core would be.
Place the BIOS in the folder where the N64 ROMS are if you are still having trouble.
Place the N64-database.txt file in the folder where the N64 ROMS are if you are still having trouble.
Locations of the BIOS files in the ROMset
The Nipponese BIOS is pifdata.bin in n64dd.zip.
The American BIOS is pifntsc.bin in n64.zip.
The European BIOS is pifpal.bin in n64_pal.zip.
Note: n64, v64, and z64 ROMS all work.