I got this to work.
Guided by what someone else had done for the other GCN Zelda OOT port (Collector's Edition), I identified a Gamecube specific header that was repeated twice in the file so I deleted it.
I then found out that the save data was byte-swapped compared to the Mupen64 PC .sra save file so I swapped the latter and that helped me identify a few key values that mark the beginning of the actual save data.
After this, it was just a matter making sure my file size and starting charcters on the converted Gamecube file were the same as the Mupen savefile.
I then byte-swapped the file and tried it on Mupen 64 PC and was pleasantly surprise to see my name on the savefile selection screen.
However, I was thrown a last curve at the end because when I frist tried the savefile on Wii64, it did not work. So, I byte-swapped the file again to return it to its original state and that did work. Strangely, Wii64's .sra files are byte-swapped compared to Mupen64's.
Anyway, mission accomplished.
If anyone ever need details about this, just PM me.
Regards.