Syntactically, it's impossible for us to know any better than you do. Both subdivisions of the sentence are possible.
However, I would intuitively go with the second one, because
It seems empirically more likely that Latin and customs are paired rather than that learning and customs are paired.
Often when a writer adds this unnecessary "also", the goal is to interrupt the closest coordination. Same with "as well as", which does the job better by introducing a bigger break.
If the writer had wanted to insist on Latin as the language of customs, they could have repeated of: "and (also) of many customs".
But these aren't conclusive reasons. Latin could well have been the language of the customs; "also" could be used for emphasis; and a second "of" is not strictly needed for the conjunction.
In a conversation I would probably have to clarify this.