Hey HB, not a problem! Once rooted you will transplant into a container and set them on the 3'x6' tables I added to your design. There they will "veg" until you achieve the desired size and maturity, then they'll go into the flower room!
Cloning is advised when cultivating for production or on a perpetual level. For that size of a flower room, even if you grew 9 plants per light (54 clones), 5-6 mother plants would be plenty and I'd keep them in 2-3 gallon pots and cycle them every 3-4 months.
Well, I'm not entirely sure what your cultivation methods include but seeds can be incredibly cumbersome for any project larger than a small tent. You'd need to buy WAY more than you'd need and consistency will be off in the flower room from seed to seed. What's your hesitation with clones?
Do you have the timeframe to be able to grow from seed each round? How tall are your ceilings? I've double stacked 3'x6' tables before using VHO T5 or 315w CMH.
The microbes will still thrive, consider Unleash organics: https://www.monstergardens.com/unleash-organic-solution-16-oz?search=Unleash&category_id=0
It offers a massive population of bacterial spores aimed at improving uptake of all micro and macro nutrients.
The application is only 1ml per...
How saturated is your Soil? What kind of soil is it? pH? You need a microbial product to bring her back, something to pump up the beneficial colonies in your rhizosphere.