Learn English – How should I phrase “Not only but also..”

Regarding your primary question of the position of 'not' following a sentence that starts with 'Not only..', the third option seems correct. Because, the verb to be negated is 'been prepared' and therefore, the position of 'not' would be right before it.

But I have my doubts whether the 'Not only..but also' sentence structure is the right choice to convey the meaning you wish to convey.

Something like...

These conditions have neither been prepared in developed countries, nor been accepted in developing countries

...feels much less complex, but conveys pretty much the same meaning as far as I understand

Edit : And as @nonchip said, omitting the 'also' doesn't seem to be good idea.

Omitting but leads to a nasty comma splice. But's role as a coordinating conjunction is to join those two independent clauses. You could, however, use a semicolon:

Not only would it provide...; it also would...

In my opinion, the quoted example ("Rowers not only face backward, they race backward.") is grammatically incorrect. I would use a semicolon or include but before they.