So in the end it was the bacteria all along!? Crazy! Good to know. Could you place your current buckets into slightly larger ones or a single large tote and screen off the roots so they wouldn't be able to grow into the new drain holes?
I came to the conclusion of the bacteria being the culprit based off my latest res change. Once the pH settled down after the 24hr climb, it's progressively been dropping now, and everything else is in line with a healthy system.
Well, I just did one bucket, and that's all I'm doing. I'll be surprised if the plant survives given the re-installation process was anything but gentle. Pretty sure I did a number on the roots near where the rockwool starter cube is. It was a complete pita.
Wet hydroton is NOT light, even only 3gal, and working in a confined space. What I ended up doing was unscrewing two of the slats under the buckets and sliding them out of the way, then sliding the bucket down off the root ball. Reinstallation was not so smooth as that was no longer an option with the new drain setup.
If it does survive, it has an upgraded drain now, and the other's roots are trimmed up to where the hole is on the inside of the bucket drain. There were a lot more than I expected, roughly 12" of roots running in the drain pipe. If it weren't for the clogging, i would've just let em run all the way to the res. Now I'm delayed on flowering for another couple weeks to ensure they recover fine, and may be down one plant, which will make this entire run a wasted effort. Learning experience, but monumental waste of resources.
Overall, a few more lessons learned:
1. Design your system for easier accessibility/maintenance. Despite never planning on vegging this system as long as I have, I could've built some "safeties" into the system for situations like this. If I continue to run a system like this indoors, I'll do a four site system, veg for a quarter of the time, and do everything better overall.
2. Bigger drain holes may be a safer bet for this style of system with cannabis if intending on longer veg times. Otherwise, more sites are highly recommended.
3. Pay attention to the people that you're ripping your system designs from. I made a mistake in not having an additional 90* bend on the inside of the pot, pointing downward, which I believe is there to prevent exactly what's happened here.