I suppose both readings are grammatically defensible, but the context suggests the authors mean “often/a lot of” rather then “well”.
“Eating well” implies either a healthy, balanced diet or having sufficient food so as not to starve. Neither really fits the context - rice will not help you much if you lack micronutrients, and there is no mention of starving or food shortage before the times of rice mixing in the text.
Rather, reading よく as “often/a lot of” ties in with the previous sentence discussing the huge popularity of sushi with the Japanese - our sentence can be read as an explanation for it.
I would even be tempted to read すし as the main subject of our sentence, carried over from the previous one:
Sushi is a Japanese food that is popular with a lot of people, young and old.
It [=sushi] has been eaten often since the olden days because rice, when mixed with vinegar, doesn’t spoil easily.
Note: sushi is prepared with rice mixed with vinegar, sugar, salt and other stuff [link]
I disagree. が explicitly links ご飯 only to the verb that follows it, 長持ちする. Thus, ご飯が is the grammatical subject of the clause:
The second clause, however, has no explicit subject or topic:
EDIT: Note that our sentence contains two independent clauses linked by a coordinating conjunction ので (“and so”). That’s why the subject of one clause is not necessarily the subject of the other.
On its own, the phrase could mean “Ever since the olden days we’ve eaten well”. It may also refer to the last explicit subject, ご飯 ("[Because rice is long-lasting,] ever since the olden days we’ve eaten it often/a lot of it). But I think the text as a whole makes the most sense if our sentence referred to the subject introduced in the previous sentence, おすし, rather then suddenly switching to talking about rice in general, only to go back to discussing sushi in the following sentence.
As for the topic/subject conundrum, I think sometimes marking the distinction between the two is unnecessary, or even potentially overcomplicating things. In our example すしは and すしが would be interchangeable:
Now, even if you speak of “sushi” in other countries it will be understood as Japanese sushi is very popular.
せかいの いろいろな 国に おすしの おみせが あります。
In various countries throughout the world sushi exists.
I’m a bit stuck on the よく in the first sentence. When I looked it up it seems to mean properly, skillfully etc. Is that to do with how well the rice and the vinegar is being mixed or is it something else?
Also can’t figure out what おみせ is. I checked the vocab list in the docs and the みせ is down as “shop”, but why is it おみせ?
Thank you for this advice. I started by jotting down on pen and paper any words I could pick out from the sentence and then translated the gaps as you suggested, so I think I’ll keep doing that. Looks like I just need to knuckle down and start working through the Tae Kim book - I have had it bookmarked for ages but only read through the opening chapters!