So does peter have his original power back and flying he gained from Nathan? Or does he have everything back. And wouldn't he be able to gain flints powers as well? I feel it's a tad unclear, could someone explain?

Well I think the only ones knowing the complete answer is the cast and crew.
But I think that the ending implied he got resetted on every ability.

He probably got reset, but the only thing we have seen so far is flying so who knows.

I think there was a hint that he got reset. after the injection he seemed to react(with the sound and vibrations) like he was using Matt's powers. Since it's easy to overload without control, and he wasn't expecting that power...

I thought we already had a thread about this?

Look at his and Nathan's conversation after escaping Pinehearst. Look at Peter's cheek. Notice something? He got the flight from Nathan and presumably pyrokinesis from Flint. His powers reset. All he got from the formula was EA.