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High Voltage Power Supply (2.5 KV+)

I need some help putting together a circuit for a power supply capable of 3000 KV / 200μA.  I found the design reference for the LT1304 capable of 1000V, but VIN needs to be capable of supporting 12VDC.  I've also seen DN1047 with a 1000V supply but I've read on the forums that adding a CW voltage doubler would probably not work due to current spikes.

My current goal is to use a power IC connected to a transformer with the secondary output connected Cockcroft Walton voltage multiplier with 6-8 phases.  I'm able to successfully get things working with the LT1304, but I need to operate with a VIN of 12VDC. Is there another IC similar to the LT1304 that supports a higher input voltage?

I've tried 10-15 different LT ICs in LTSpice, but all of had huge current spikes when trying to ramp up the output voltage.  When using the current limit function (usually on the drain of the MOSFET) I can limit the current on the primary side of the inductor to safe levels, but the consequence is there is not enough energy going into the transformer due to the small minimum on times of most of the current Linear Tech ICs, ranging around 110-300μs.  

So is there a Linear Tech IC that has a larger minimum on time that would be suitable for this application?  Is there another design reference of a circuit that supports voltages in the 2.5-3 KV range?  Any help is greatly appreciated.