The motto I learnt about sieving was the following: upper bounds are easy, lower bounds are hard. Thus, since we are interested in bounding $\pi_{r,2}(x)$, it seems that we are in good shape.
However, there is a subtlety here. Let $\pi(x,z)$ denote the number of integers $n$ less
than $x$ such that every prime factor of $n$ is at least $z$. It's clear by the
argument of the last paragraph that
$\pi_r(x) \ge \pi(x,x^{1/r})$. One might imagine that these numbers are roughly of the
same magnitute. However, it turns out that $\pi_r(x)$ is much bigger than $\pi(x,x^{1/r})$.
The latter is comparable to the number of primes less than $x$, where the former has
an extra factor of $(\log \log x)^{r-1}$. The reason is that $\pi_r(x)$ is dominated
by numbers with (a few) small prime factors. In fact,
as Kowalski pointed out to me, it is not even obvious that
one can easily obtain the
correct upper bound for $\pi_r(x)$ simply by sieving over primes.
From the asymptotic for $\pi_{r}(x)$, one expects that
$$(*): \qquad \pi_{r,2}(x) =^{?} \ O\left(\frac{x (\log \log x)^{2r-2}}{(\log x)^2}\right).$$
(I expectEDIT: My resident expert reports that suchthis is known. Here is a result, perhaps slightly weaker,sketch of the idea in the simpler case where we want to count pairs does exist$n$ and $n+2$ where $n$ is a $2$-almost prime and $n+2$ is prime.
in the literatureFirst, I will update this answer when Ifor a small prime $p$, we want to find an upper bound for the relevant
linksnumber of - actual experts$n < x$ such that $n$ is divisible by $p$ and both $n/p$ and $n+2$ are being consulted asprime. This is a similar problem to counting twin primes, and in a similar way one obtains a bound of the form $O(x/\log x)$ (key point: the implied constant does not depend on $p$). If we speakwish to bound the number of pairs $(n,n+2)$ such that $n+2$ is prime and $n$ is a $2$-almost prime, we may instead count the triples $(p,n,n+2)$ where
$p < x$ is prime, $n < x$ is divisible by $p$, $n/p$ is prime, and $n+2$ is prime. If for each $p < x$ we have a upper bound of $Ax/\log x$ (for the same $A$), in total we obtain the upper bound:
$$ \frac{Ax}{\log x} \cdot \sum_{p < x} \frac{1}{p} \sim \frac{Ax \log \log x}{\log x}.$$
Of course, the devil is in the details! END EDIT)
All one needs to answer 3) is that
the exponent of $\log(x)$ in the denominator is $> 1$.