So, I managed to borrow a wiimote, and freed a chunk of memory blocks, indeed that was the issue, I had around 150 blocks free, getting over the number you suggested worked like a charm, thanks!
Also, Banjo Tooie works almost perfectly now, enable both sets of textures and toy with the audio section a bit, to get the random speedups of the soundtrack to stop.
Only issue is that the game is running a bit fast in some areas, but nothing that really hampers gameplay.
One example is Mayham Kickball minigame, before it was impossible to play it as the colission with the floor gave away and you sorta sank onto the ground, as of the latest rev, this doesn't happens anymore!
@DarthBellic because for the correct functionality of the NAND pagefile feature.
I know that the entire Mario Party game series (for the N64), Conker's BFD, Donkey Kong 64 and other N64 games required this function in order for run in Not64, since of the poor RAM memory of the Wii (64 MB).
EDIT: That's because the NAND pagefile function consists in use the Wii's NAND memory as if it were a "virtual RAM memory", for avoid a possible overload of the real pyshical RAM memory and, at the same time, run the games at a playable speed.