Great news! I managed to remove the mold AND the stains from all my diapers and have been mold-free for 2 weeks!
Here is what I did (in case it helps others...)
1) Replace my washer. In my case, the washer was the cause of my mold issues. (BTW, my new washer/dryer rock!)
2) Wash everything(diapers, wipes, wet bags) on a hot cycle with 1/4 cup bleach. This had to be done for my own peace of mind to ensure the mold was dead.
3) Soak everything in Oxiclean and hot water to remove the stains. In the natural fiber diapers, the stains were gone after a 24 hour soak. My minky Tot Bots had to be soaked 2-3 times for 24 hours each soak in order for the stains to go. I knew I was risking damage to my diapers by soaking so long, but I needed those stains gone or I was going to toss the dipes anyway. I just couldn't bear putting mold stains on my LO and I wanted to know that if I ever saw a spot again that it was new!
4) Hot washed everything and did 8 rinses to ensure the chemicals were rinsed away (LO has sensitive skin).
I was a little scared that I might have killed my diapers, but I have been using them day and night for two weeks and they are perfectly fine. The pul looks and works awesome, absolutely no issues and not a single trace of mold.
The only casualties were my Planetwise wet bags. The colors faded and they have been leaking. But a small price to pay considering I thought I would have to toss everything and start new.
Yipee!!!
One more note: I have read that some people have had success removing the stains with a lemon juice/salt paste and sunshine. This did not work for me, I think because my stains had set in the dryer. Might be worth trying before Oxiclean though as it wouldn't be as hard on the diapers!