The only comment I would make concerns vacuuming/not vacuuming the substrate. I have maintained planted tanks for more than 15 years and have always done some weekly vacuuming of part of the substrate; I have never uprooted the plants.
First, what needs to be done partly depends upon the bioload in the particular tank. My aquaria are heavily stocked and a fair amount of detrius accumulates on the substrate over a few days. I have corys and aspidoras that constantly root through the substrate [the aspidoras in particular, they act like loaches, digging headfirst half their body length into the substrate searching out tidbits of food]. Aside from the mess, I prefer to keep a cleaner substrate for them; others on this forum and elsewhere have suggested that barbel degeneration is possibly due to detrius (and nitrate buildup) at the substrate, and while I am not saying yea or nay to this, it makes sense and as I can prevent it I would rather do the vacuuming than risk my fish.
Second, the method. I only clean the substrate I can see from the front, never bothering with the back corners and along the back wall where the plants are thickest. I move the Python over the substrate at the surface so anything lying thereon is normally sucked up. The gravel is not displaced, and the plants do not uproot. In the areas that are more "open," and particularly where I feed tablets for the corys, aspidoras, farlowella and whiptail, I do go into the gravel about an inch. The amount of mulm that comes up is considerable. I do not think it prudent to leave this permanently. There are many areas I never touch and the aerobic and anaerobic bacteria undoubtedly work their marvels in those areas. I monitor nitrates, they are constant at 5 ppm. The pH is constant at 6.2 to 6.5 with the diurnal variation.
I have mostly rooted plants and would never uproot them; stem plants of course have small substrate root systems and do easily come up with any disturbance, but I don't get around to where the Pennywort is rooted, but in any case I pull it up every 2-3 weeks to trim the shoots or they would cover the tank, and I prefer to keep the active growing tips rather than old thick stems.