Here's one suggestion if you are interested...I have done this in the past when I unexpectedly got 3 females out of 10 plants. I took clones as soon as I could and then topped the mothers to slow them down (I find topping of FIMming slows them down by about a week. Then I popped the moms into flower. Then when the clones root, I gave them a shortened veg time and put them into flower 1-2 weeks later than their mothers. If you are flowering your seed plants earlier than they can give clones...no worries. I routinely take clones up to 14 days into flowering. Just takes them a little longer to root.
That way at least I had a full flower room most of the time and harvested the seed girls and then their clones 2 weeks later. The downside is that you have slightly different nute schedules at some points (eg you start flushing half your room while still ferting the other half) but as long as you keep good notes about who gets what, its pretty straightforward.
This works especially well with Sativa strains as they seem to require less veg/rooting time before going into flower as clones. Kali Mist for instance, I have flowered 5 days after the clone rooted.
Sorry I can't help you with your new probs as nutes/PH/deficiencies and all that stuff is my achilles heel. I will say though that I have a lot of minor issues like you are seeing all the way through and I still see some pretty damn nice buds. So just be careful not to get discouraged or be tempted to fuss over them too much.
Thanks for the advice, I'll consider it. One plus is that we won't have to worry about different nute schedules for the most part since we're all organic and we plan to water with a tea of LK, EWC and molasses and not much else (we might do a guano tea watering right before they enter into flower, and about 2 weeks before harvest). But they won't need any flushing, that's for sure!