nintendont only has one version there is no such thing a a wii version lol same version is for wii and vwii on wiiu
latest is nintendont v 187
link here
https://nintendon-t.googlecode.com/svn-history/r187/trunk/nintendont/boot.dol
get that
On your wii menu just press your wii sinc button and do the same on the wiiu pro controller, the wiiu pro controller will flash for some instants and then shutdown this means it has synced
Now do as you normaly do launch a game in nintendont when the game is running just press any button on the wiiu pro controller like the A button and the controller will sinc up and be usable.
seems your not using the lastest version? i putted a link here latest is 187, it seems your using an really old rev
Also there is no such thing as a gc iso that is 1.46 GB, full GC isos are all 1.35 GB not sure where you got 1.46 gb isos lol.