Consider Euclid's method for greatest common factor

[ceautery]

You're doing a lot of unnecessary processing for finding the gcd. Consider using something like the following instead:

function gcd(a, b) { return b ? gcd(b, a % b) : a }

I think this also obviates the need for calculating the prime factors.

[ceautery]

Looks like something similar was implemented a couple weeks after I opened this. Closing!