Food derived probiotics can be taken whenever you want; the other capsule probiotics should be taken on an empty stomach. I personally take my probiotics with my meals (personal decision).
I’d ask able why you should start after 2 weeks; he developed most of the protocol.
If you want to do everything all at once (antifungals, probiotics, new foods) you are welcome to go for it; this is how I started out the diet because there was no protocol when I started nearly a year ago. Able promotes a cautious approach and I promote a go for it approach.