Just submitted my PhD thesis after four years of doing research at Oxbridge in Molecular Biology. My supervisor told me two months ago to submit the thesis for MPhil instead of PhD because I don't have enough data for PhD (in her opinion). The PhD was nightmare:
-I had personal relations problems with my supervisor (at my first year she constantly told me that I am stupid, have bad memory and that I should get off a PhD and should not deal with science at all - I started to avoid her).
-The project I was doing had no clear question,often based on the artefacts generated by the previous student (so despite being at high-profile institution, our lab has a very poor publication record).
- got very few training in the model organism I was studying.

But. I really love science and want to stay in it. I had a record of success in science: I got funding both for first and second degrees, several awards. In terms of research I got a 5-month internship before starting PhD and initiated the project that can be potentially a Nature paper (now in the first round of revision in Nature with positive reviews, I am a second author out of five).

In summary:
-Potentially failed PhD at high-standard institution with very average references from a PhD supervisor (something like "smart, able to generate new ideas, good at molecular biology techniques, but not attentive to details and not always setting up the experiments properly, not able to work independently and need retraining").
-No experimental skills that are in high demand.
-A glowing reference from the second referee (internship supervisor, from the work that has been done 4 years ago).
-No publications so far.

I consider applying for a second PhD as I became interested in Neurobiology during my PhD. I am 27.

What is the best way to describe my experience during PhD (or MPhil, if I get no PhD)?
What is the best strategy to apply? Or should I get an unrelated to research job instead?