Decided to basically leave the hardscape how it was and just move the plants around a bit to give them access to more light, and let them start rooting and get established.
I gave it a few days to see what effect the change in available light had on the plants. Everything started looking better, except the bolbitis, which was still slowly melting. Granted, it's still sitting in the corner, furthest from the light...but from what I understood it doesn't really do well in high light. In fact, at the lfs, the leaves closest to the light were already melting on some plants, especially if they were emersed. I'm thinking it's more due to the roots of the plant. I tied the rhizomes to rocks, and buried the roots a bit into the substrate, leaving the rhizomes exposed. However, most of the roots on the plant were pretty dry (basically dead) when I got it at the store. Since they were all so deeply rooted and intertwined under the substrate at the lfs, I think most of any potential new growth on the roots didn't come up with the plants. I'm hoping it eventually starts to do better...but I'm doubtful at this point.
Once I was convinced that the lighting was good I waited a couple more days. Noticed that the stem plants were rooting nicely, but did start to notice deficiencies in the foliage. So, I started dosing micros with Flourish to see what effect that had.
A couple days later and I noticed a lot more new growth on everything...well...except the bolbitis
I've been testing the water's pH, ammonia, nitrites, and nitrates on a daily basis.
pH = 7.4
Ammonia = 1.0ppm, fluctuates slightly throughout the day, but not by much. I had a "peak" of about 3.0ppm about 4 or 5 days ago, but it's been going down since then, until stalling at 1.0ppm for the past few days.
Nitrites = 0
Nitrates = Well...hard to tell. I'm using the API master kit. Comparing a tube of tap with the tank water when I test them simultaneously...there is a definite difference in color. But, the kit's first reference range is at 5.0ppm, and it's certainly not that high. I don't know the accuracy of this estimation, but I'd say maybe 3.0 ppm?
dKH = 4.0
dGH = 5.0
Right now, I'm dosing with 0.6ml Excel daily, and just started dosing with 0.7ml Flourish (weekly?) a couple days ago. Not sure if I'm going to need to dose weekly, or 2x a week.
Oh, and to satisfy my urge to stare at the tank at night before bed, I also added an LED strip for a moonlight effect. I aimed the beam up toward the hood / DIY reflector so that it gives a nice glow rather than a bright beam traveling into the tank. I love the effect, it's actually a lot more subtle in person, but I adjusted the exposure for the photo.