I don't think they're that critical. Having a balance within a town section is important if you're going to farm the dungeon there, but the fact is the homestead is a safe motherland for growing new runeys as long as it's continuously cultivated. Having runeys everywhere, from my understanding, is NOT critical; what's important is to have the runeys balanced within a single town section that you intend to farm (ex: Mist's House area affects crops in Green Ruins).
Summer crops take ridiculously long to grow, and they're easy to lose track of when you deviate from your daily routine; it's too easy to neglect crops for a day and make growth rates seem longer than you expect.
Once Winter rolls around and your farm can't grow anything, then your Homestead runeys will start to take a hit, and you should be prepared to grow crops elsewhere anyway. Or FISH! Runeys don't affect FISH! When Spring arrives, you can try to repair the ecosystem then.
The benefits of having an abundance of runeys are creating Miracles and forming Rune Stones.
Only my Homestead and Mist's House are being maintained. The lake has a bunch of Water Runeys, and the Mountain Road has a bunch of Tree Runeys, cuz that's how nature happened. Everything else is Zombieland. If I chose to redistribute my Homestead Runeys, I just leave about 10 of each behind, then start dropping Runeys elsewhere based on where their population growth is favorable.
Actually, it's the other way around: the runeys for a particular zone are irrelevant: it's the aggregate that matters. Your farm can be barren, but as long as the other zones are in prosperity, you take advantage of the prosperity rules.
So yes, Mop_it_up, you ARE in trouble.
Fortunately, there are a few things you can do to fix this. First, take advantage of your farm being a free zone, so as to grow more runeys. Second, remember that any 3x3 plot ON YOUR FARM that you don't harvest creates an extra runey at the end of the day (unharvested plots in dungeons only create Rune Spirits, which you don't care about right now). Third, remember that the first eight days of each month are "free" days, where runeys don't kill each other; in fact, you GAIN one of each runey in a zone.
So STOP HARVESTING IMMEDIATELY. Let your farm produce runeys. Hold onto rock and grass runeys for the rest of the month. In the meantime, move one (and only one) tree or water runey into any zone that is in runey extinction (this prevents the penalty on growing crops: one of any runey is enough to avoid the penalty. But remember to replenish each zone ASAP!).
On the last day of the month, harvest all but one of the rock and grass runeys on your farm. On the first day of the next month, move ONE rock and ONE grass runey to as many different zones as you can. This is so you can take advantage of the "one new runey a day" rule. At the end of the eigth day, harvest all your grass runeys from all but one zone. Start a grass factory per Gamefaqs' suggestion (preferably in Mist's zone) to increase your Grass supply, and nurse the factory as needed. Remember to keep an eye on the other zones, and make sure to replenish one random runey in any zone that goes into extinction.
Rock Runeys are trickier: I advise harvesting all of them until you have a decent supply of grass runeys beyond what you need for your factory. Pick a Rock-friendly zone (I like the Town Square). If possible, get it into prosperity by adding 35 of each type, and replenish the two lost grass everyday (while harvesting some of the other three types).
If you can't reach prosperity, dump as many grass as you can afford, an equal number of tree, as many rock as you can, and a handful of water runeys into the zone, and keep a very close eye on the runey balance. You'll probably need to trim the water supply, while replenishing the grass.
Alternatively, you could harvest all your runeys after the 8th of Winter, then take advantage of the 8-day rule come Spring. That should give you a running start for that month, with the only cost being that your crops in the dungeons will grow pretty slowly.