1) It appears that your build system did not build an ELF for Linux, it built one for the N64 (see the "mips-" in front of the compiler's filename? that means the system is cross-compiling for the MIPS architecture which is the N64 archtiecture), thus why you're receiving a Z64 file and can only run it via PJ64. OoT does have a decompilation/port project like SM64 right? If it's only a decompilation/recompilation project you're only going to get a N64 rom.
2) You're running on a 64-bit processor, the build system WILL use 64-bit GCC but that will call the 32-bit versions as needed. Not sure if you're still stuck attempting to install 32-bit packages, but after using dpkg --add-architecture, you need to perform a apt update or apt-get update. If you mean that your built application is still attempting to use 64-bit libraries, you need to ensure that you have the 32-bit versions of those libraries installed, not just their -dev packages. Unfortunately, unless you run a 32-bit chroot, this may be impossible as usually Debian systems do not do multiarch and will attempt to replace a 64-bit package with a 32-bit one. Instead what you should do is compile your application for 64-bit instead (really, is there a reason to compile for 32-bit?)
Edit: Added some more to number 2.