Its not quite that easy to just compile it withhin Linux. It doesnt matters much which compiler was used, but Windows has a completely different interface as Linux. Not just the GUI is different to code, but everything that relies on communication with the System.
The C++ compliance between System only goes as far as basic input and output( reading/writing files and handling a Console, ie: Dos Prompt )
its mainly dependend on how PJ64 was wrote, if Zil wouldve seperated OS-Dependend Source and OS-Independent Source, then just a part of the Emu wouldve to been rewritten. From what ive seen thats not the case.
Also theres no way to compile my Plugin for Linux, not only because the GUI wont work, but also because Linux doesnt have a DX8-Interface - which pretty much limits the usefull source to the Gamepak Handling.
IMHO, it would be better to start from scratch and use only Parts of PJ64 which are independend of the OS