Since we talk "strategies" here, and specifically, "farms or biowells" question, - my answer would be:
Farms.
Points given by all the gentlemen above are sure solid, academy spam is boringly popular way to do things "right" (i don't question its popularity, though i do question the method itself; but, offtopic). In the scope of this topic, though, i understand i should compare just two said improvements: biowells and farms. Without considering other options (other improvements).
Now to answer questions asked in the 1st post.
1. If/when health is no longer an issue, - there is no reason to use Biowells. Quite the opposite, there is the reason not to use them when health is not an issue: maintenance cost for each biowell, last i checked, is 2 energy per turn, while for farms it's 0 energy.
2. 7-8 cities is quite OK. As for what you could possibly do "wrong" - i guess it's +health virtues. You need either Magnasanti and good production in your cities (read = tons of internal trade) to make lots of buildings; or you need at least two other good (scaling up as you develop) +health virtues. That's "ASAP". Considering effective difference between -40 or lower health colony and +25 or higher health colony, we can see that the difference is huge when all changes are considered together. Virtues allow to make TONS of health out of things you "do anyways" (basically, you build things "anyways", it's either industrial development, or huge and active all the time army (Might tree), or even if you know what you're doing - both to some degree). And both Might and Industrial virtue trees have strong +health virtues (especially the latter), so virtually you get tons of +health "for free" from those virtues (in terms of _tile_ development, i mean). In my opinion, realizing this massive +health boost which brings your colony from much negative health into far positive (which boosts "everything" much) - is the primary priority in developing one's virtues. May be you're not doing this? If so, perhaps try. That said, i mean to "hurry up" to some most powerful +health virtue(s), but i don't mean being "scared" by being in negative health while you expand _before_ you got those mighty +health virtue(s). Instead of spending time building biowells which could keep you in good (above -5) health for a few dozens turns, it seems much more efficient to expand and grow despite unhealth - by the time you solve your health problems with virtue(s), that expansion and growth created a larger "base", i.e. more city and higher population, which with now-good health boosts all things further massively and quickly.
3. Ratio between Academies and +food improvements: no such thing exists, i think. No constant ratio. It depends on present resources and terrain, and how trade developes, on per-city basis. It also varies with time: the closer you are to the victory, the less sense there is to have any extra food if you can "replace" it with more +science, since the less turns remains till the end of the game, the less "use" you'll have from extra growth, results of which will have less and less time to "work" for you. This is for usual higher-difficulties gameplay "just gotta make a victory" game, of course; long plays aimed at much gameplay after "one more turn button" are of course different.
To sum up - i think, forget biowells entirely, do significant effort to get to Magnasanti (best case for health) ASAP, possibly even without taking a free settler from Prosperity in the start of the game, and just spam academies on most tiles, doing farms here and there as much as any specific city requires to stay growing quite fast early, still grow somewhat mid-game, and just stay not starving late-game. Replace farms with academies when appropriate to keep this general "deceleration of growth" as you approach end-game.
Everything above is just my (far from expert) opinion, of course, and could be incorrect; i hope it's useful, though.