the extraction seems to be generating floating nodes due to the connection of the extracted capacitances. This causes issues with ngspice. Is there any way to prevent floating nodes / automatically add some large resistance to ground?

I use something like

.option RSHUNT = 1e20

. This creates a resistance from every point in the circuit to ground, but it's so ridiculously large that it has no impact on circuit operation, other than to keep ngspice from complaining about floating nodes.