just got around to passing this thought through my head. i started the new seedlings with my clones from the infected mothers before posting this thread. time to start a couple new ones and keep them completely separate.
Sounds like you are due for some new genetics or a reboot of your current. Are you familiar with TCC Tissue cell cloning? It's like rebooting the genetic system of your strain. Might be something you want to look into. If you want to revive vigour in your plants the most common factor for most people is not enough of completely void of mineral and rock dust... It's what your soil needs to deliver food to your roots. It's a catalyst for microbial lifeforms
Or wait till harvest and reveg the mothers. Once they are harvested, they wont be fertilized. And this time, you can just use the pollen from your former males for your cross experiments.
what a difference after only this short time! every plant is deep green, first set has started stretching, clones are showing better/thicker roots, new moms are throwing off bigger sideshoots, old moms are looking much much healthier. will post pics in another week or so to show them all at the same stages of growth (exactly 3 weeks from previous pics)