If it indeed had been isolated, as so many sites like to claim, why did it take over a year to determine that the PCR test was so ineffective that it couldn’t distinguish between what is known as Covid (and other names) and influenza?
It didn't. When the CDC got the EUA for that test they made it clear it was to detect SARS CoV-2 only.
That's what it did and it never confused the influenza virus with the coronavirus causing Covid.
There are now approved test panels that can identify SARS CoV-2, influenza and other respiratory virus from a single sample and the CDC is recommending labs use one of those.