Disclaimer: I am not an expert, only enthusiast.
Hi, i want to experiment with a small scale axial flux motor and a single coil.

The first question is what should be the polarity of the magnets? Same or alternating?
The second question is what should be the shape of the coil. Is a core needed?
The output should be about 5 Volts.

 

Since we don't know your aims and you state that you want to experiment, you would be better placed than this forum to answer all the questions you are asking. A bit of Googling should find you lots of references to axial flux motors/generators.
Your thread title refers to a motor, but you mention an output of ~5V. Is your 'motor' in fact to be used as a generator?

 

Disclaimer: I am not an expert, only enthusiast.
Hi, i want to experiment with a small scale axial flux motor and a single coil.
The first question is what should be the polarity of the magnets? Same or alternating?
The second question is what should be the shape of the coil. Is a core needed?
The output should be about 5 Volts.

May be this thread will helpful for you:
https://forum.allaboutcircuits.com/...ing-a-brushless-generator.145423/post-1256308

 

Since we don't know your aims

I was thinking blowing up the Pentagone.

A bit of Googling should find you lots of references to axial flux motors/generators.

I did some research but all the references were at large scale and were using multiple coils generating multiphase current. So i couldn't get all the answers.

Your thread title refers to a motor, but you mention an output of ~5V. Is your 'motor' in fact to be used as a generator?

Yes, actually i want to use it as a generator.

 

Yes, actually i want to use it as a generator.

Then look Google Hugh Piggott or brake drum generator. Piggott is has proven designs that work. At one time(don't know if it's still true though) his generator was his only source of electricity.

https://www.google.com/search?q=hug...hUKEwjju_214-_zAhXIl3IEHaWaAZQQ4dUDCA0&uact=5