best way to rectify 30kv flyback output?
1N4007 are not really suitable for such a high frequency circuit due to their slow recovery time (microseconds). At mains frequency you could use series string. 
You could try a series string of UF4007 diodes (75ns recovery time). 

You can buy packaged 80kV 200mA 100ns rectifier stacks for about $30 if you look around.