You first job and expenditure is to get your house up to NEC 24 electrical codes to very substantially reduce the risk of this happening again. So this means SPD-1 surge protections at the entry of electrical service to your home. Then you need SPD-2 surge protection at every panel.
We need more information about those subs. Are they ported or sealed? If they are sealed then you need original plate amp replacements. If you want to use an external amp then you need to disconnect the sub driver from the plate amp, and connect the sub driver directly to the speaker terminals of your power amp. The plate amp needs to be put back in, or the hole where is was closed up.
Now you do need to check the impedance of the sub driver, as some subs have drivers of unusual impedances.
The last issue is that the drivers may very well have been damaged in the lightning strike, and may well have damaged voice coils with shorted wire turns. So you need to check the DC resistances of the woofers VCs. The DC resistance is usually about 60% of the driver impedance at least, and anything less indicates a partially fried VC. The DC resistance can be as high as 90% of the impedance, but this is unusual. It generally is very close to 60%. The chance of the driver being fried is high after an event like this.