Building a micro generator, I need to account for the pulsing DC after my 3 phase diode bridge
If what you say is correct, I would recommend that you use a load of about 10 ohms (150 watts).  This should keep the spikes below 500v which will allow you to use a 10 micro-farad 600V AC capacitor. Check the results with the O'scope and see if that takes care of the problem.