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Should I use the Spooky2 Boost to drive the input to the scalar when running in rife mode? Or which output of the GX should I use?
No. Do not use a boost. Use square wave, 5v, 100% offset for the modulation input. Out1 or Out2 are ok, but we generally use Out2 because that same output is used for modulation for Spooky2 Plasma.

Can I use an XM generator or only Gen x?
Both XM generator or only GX can be used. But you can use GX without a computer.