I believe I saw precisely this tricky part you mentioned, and decided to only write the sketch because of it. Let me add some details to clarify.
I'll use the same $g$ as defined in that sketch:
Let $\frac{f(n)}{n}=\frac{\mu^2(n)}{\phi(n)}$. Set $g(n)=(\mu * f)(n)$ so that $f=(1*g)$.
Then, as mentioned in the sketch, $$g\left(p^{k}\right)=\begin{cases}
\frac{1}{p-1} & \text{ if }k=1\\
\frac{-p}{p-1} & \text{ if }k=2\\
0 & \text{ if }k\geq3
\end{cases} .$$
Let $G(s)=\sum_{n=1}^\infty g(n)n^{-s}$. This $G$ is also slightly different from that defined in your question.
Bounding the Error Term
Our goal is to prove a bound on the following sum:
Goal: Bound $$\sum_{d>x}\frac{g(d)}{d}.$$
Let me begin with a lemma.
Lemma 1: We have that $$\sum_{j>y}\frac{1}{j\phi(j)}=O\left(\frac{1}{y}\right).$$
Proof: We can bound this by using a Riemann-Stieltjes integral and integration by parts. Define $S(t)=\sum_{n\leq t}\frac{n}{\phi(n)}.$ Then $$\sum_{j>y}\frac{1}{j\phi(j)}=\int_{y}^{\infty}\frac{1}{t^{2}}dS(t)=\frac{S(t)}{t^{2}}\biggr|_{t=y}^{t=\infty}+\int_{y}^{\infty}\frac{S(t)}{t^{3}}dt.$$ Since $S(t)=\frac{315}{2\pi^{4}}\zeta(3)t+O(\log t)$, as shown in On The Mean Value of a Multiplicative Function, the lemma follows.
In the prime-power break-down for $g$, note that $g(p^r)$ is very small for $r=1$, close to $1$ when $r=2$, and zero otherwise. This means we need to split out the squares.
For every integer $d$, let us split $d$ into its power-free part $k$, defined as $k=\prod_{p|d,p^{2}\nmid d}1$, and its powerful part $l$, defined as $d/k$. Then we have $d=k\cdot l$, and $g(d)=g(k)g(l)$. Thus we are trying to bound the sum $$\sum_{\begin{array}{c}
lk>x\\
k\text{ pf-free}\\
l\text{ powerful}
\end{array}}\frac{|g(kl)|}{kl}.$$ Since $g(p^{r})=0$ for any $r\geq3$, $l$ must be a square. Also, we know that $|g(j^{2})|\leq\frac{j}{\phi(j)}$and $|g(k)|\leq\frac{1}{\phi(k)}$. Thus, we can drop the condition on $k$ to upper bound the sum, and we have $$\sum_{d>x}\frac{|g(d)|}{d}\leq\sum_{j^{2}k>x}\frac{1}{k\phi(k)}\frac{1}{j\phi(j)}$$ $$\leq\sum_{k=1}^{\infty}\frac{1}{k\phi(k)}\sum_{j>\sqrt{\frac{x}{k}}}\frac{1}{j\phi(j)}.$$
Applying Lemma 1, we have that $$\sum_{d>x}\frac{|g(d)|}{d}=O\left(\frac{1}{\sqrt{x}}\sum_{k=1}^{\infty}\frac{1}{k^{\frac{1}{2}}\phi(k)}\right)=O\left(\frac{1}{\sqrt{x}}\right)$$
The other sum with $\log d$ follows similarly.
Alternative: We could instead apply the Riemann-Stieltjes integral and integration by parts directly to $g$. Let $S_g(x)=\sum_{d\leq x} g(d)$. Then $$\sum_{x>d}\frac{g(d)}{d}=\int_{x}^{\infty}\frac{1}{t^{2}}dS_{g}(x)=-\frac{S_{g}(x)}{x^{2}}+\int_{x}^{\infty}\frac{S_{g}(x)}{t^{3}}dt.$$ The upper bound we desire would then follows from $$\sum_{d\leq x} g(d) = O(\sqrt{x}).$$ As before, splitting into "powerful-free" and "powerful" would directly prove this final bound.
Clarifying the Sketch
In this section, I'll add some more details to the sketch in the other answer. We are trying to prove:
Theorem 1: We have that $$\sum_{n\leq x }\frac{\mu^2(n)}{\phi(n)}=\log x+\gamma+\sum_{p}\frac{\log p}{p(p-1)}+O\left(x^{-1/2}\log x\right).$$
First we'll prove the following proposition:
Proposition 1: We have that $$\sum_{n\leq x}\frac{\mu^{2}(n)}{\phi(n)}=G(1)\log x+G'(1)+\gamma G(1)+E$$ where $$E=O\left(\log x\sum_{d>x}\frac{|g(d)|}{d}+\sum_{d>x}\frac{g(d)\log d}{d}+\sum_{d\leq x}|g(d)\right).$$
From this proposition, using the arguments above about the error terms, we arrive at the theorem.
Proof of Proposition 1:
Observe that
$$\sum_{n\leq x}\frac{\mu^{2}(n)}{\phi(n)}=\sum_{n\leq x}\frac{(1*g)(n)}{n} = \sum_{n\leq x}\frac{1}{n}\sum_{d|n}g(d)$$
Rearranging the order of summation, this becomes:
$$\sum_{d\leq x}g(d)\sum_{\begin{array}{c}
n\leq x\\
d|n
\end{array}}\frac{1}{n}=\sum_{d\leq x}\frac{g(d)}{d}\sum_{k\leq\frac{x}{d}}\frac{1}{k}.$$
At this point, we may use the fact that $$\sum_{k\leq\frac{x}{d}}\frac{1}{k}=\log\frac{x}{d}+\gamma+O\left(\frac{d}{x}\right)$$ where $\gamma$ is the Euler-Mascheroni constant. This yields:
$$\sum_{d\leq x}\frac{g(d)}{d}\log\frac{x}{d}+\gamma\sum_{d\leq x}\frac{g(d)}{d}+O\left(\sum_{d\leq x}|g(d)\right)$$
Expanding $\log(x/d)=\log(x)-\log(d)$, we arrive at
$$\sum_{n\leq x}\frac{\mu^{2}(n)}{\phi(n)}=\log x\sum_{d\leq x}\frac{g(d)}{d}+\sum_{d\leq x}\frac{g(d)\log d}{d}+\gamma\sum_{d\leq x}\frac{g(d)}{d}+O\left(\sum_{d\leq x}|g(d)\right).$$
That proves Proposition 1.
To prove the Theorem from Proposition 1, one needs to bound the sums in $E$ as was done in the first section above.
See also:
These two answers which use very similar techniques: