Lets say i am 2nd to start. My opponent on his first turn played, lets say, 3 foundations. It's my first turn now, Taki's ready but i have no foundations yet. Can i play her F ability thus turning one of my opponent's foundation face down and my opponent turning none on my board?

Yes.

Follow up question, if you use taki's E on an attack, can you choose for it to go to momentum?

Taki doesnt say may so i assume that means that you have to put in down as a foundation

it dose not say "you may" so it becomes mandatory

I just wasnt sure of order. If you have the option of adding it to your momentum before the floating effect trigger hits than it wouldnt be there to to your staging area.

it says at the end of your turn so lets just say that it happens when the end step begins before you start clearing cards normally?

Actually Taki specificies that it's during the End Phase, rather then the end or turn. So pretty sure there's no choice involved (or rather you've already made the choice when you use her enhance).