Selecting the right PMDC motor and battery
My first question is: Is it best to use a Permanent magnet DC motor as
  a generator, or an Alternator?


An automotive alternator is probably more power fuel than you need and more complex to use that you would like.

A permanent-magnet DC motor with a commutator would probably be ok. You may also want to consider a 3-phase brushless DC motor. That is essentially the same as a permanent-magnet synchronous motor. It would generate AC, but it would be quite efficient and easy to rectify to DC.


  What other components are needed in the circuit between the motor and the battery?


You need a voltage converter to convert the variable DC from the generator to the battery charging voltage. You also should have a charge controller that could be combined with the voltage converter.


  And what kind of efficiency can i expect from each component


Generator: 75 - 90+%

Rectifier, converter, charge controller: 80 - 90+% combined

Mechanical system: 85 - 97%

The system efficiency curve vs. speed starts at zero speed zero efficiency, then rises, rapidly at first, to maximum efficiency at or near maximum speed.


  Is it possible to charge a battery with an unstable voltage?


Some variation is ok, but you will need a voltage converter and charge controller to get the voltage into acceptable limits and control the current.