Your hope seems unsatisfiable. Let $k=2$, $m=1$, $p = 2$ and $q = 10$. Then
$$
3q-4p = 22 \text{ and } \\
7 k^2 \cong 6 m^2 \cong 6 \pmod{22} \text{.}
$$ Furthermore, both $22 \neq 1$ and $22 = 2 \cdot 11$ has no prime factors of the form $4n+1$.
Note that since both $k^2$ and $m^2$ are obviously quadratic residues modulo $3q-4p$, it must be that $6$ and $7$ are both quadratic residues or are both quadratic nonresidues modulo $3q-4p$. Only about 50% of moduli have this property. So it would seem that for half the choices of "generic integers" $p$ and $q$, there exist satisfying choices of $k$ and $m$. This doesn't tell you about the prime factorizations, but by reasonable counting methods, much less than half the integers factor only over primes congruent to $1$ modulo $4$.
A search through small moduli for those having $-14 \times 3^{-1}$, $9 \times 2^{-1}$, and $7 \times 6^{-1}$ as quadratic residues (actually, I only checked that the Jacobi symbol of these three residues was positive, which can give false positives below for composite moduli) turns up the following moduli:
17, 25, 41, 89, 121, 169, 185, 193, 209, 257, ...
all of which are congruent to $1 \pmod{4}$, but don't necessarily factor to primes with the same residue. For instance $121 = 11^2$ and $11 \cong 3 \pmod{4}$.
I like your idea of investigating for which moduli $-21 = -1 \cdot 3 \cdot 7$ is a quadratic residue. If the Jacobi symbols for each prime factor of $n = p_1^{\alpha_1} p_2^{\alpha_2} \cdots$ (where we assume each of the $p_j$ are distinct) are $1$, then $n$ will be a modulus for which $-21$ is a quadratic residue. It is convenient to dispose of $p_j = 2$ immediately: $-21$ is a quadratic residue modulo $2$, but not to any higher power of $2$. \begin{align}
\left( \frac{-21}{n} \right) &= \left( \frac{-1}{n} \right)\left( \frac{3}{n} \right)\left( \frac{7}{n} \right)
\end{align}
Now $\left( \dfrac{-1}{p_j^{\alpha_j}} \right) = \begin{cases} 1^{\alpha_j} = 1, & p_j \cong 1 \pmod{4} \\ (-1)^{\alpha_j}, & p_j \cong 3 \pmod{4} \end{cases}$. Also, $\left( \frac{3}{n} \right) = 0$ if $3$ divides $n$ and $\left( \frac{7}{n} \right) = 0$ if $7$ divides $n$, so $n$ is not divisible by $3$ or $7$. From quadratic reciprocity, $$
\left( \frac{3}{p_j^{\alpha_j}} \right) \left( \frac{p_j^{\alpha_j}}{3} \right) = \begin{cases} 1^{\alpha_j} = 1 , & p_j \cong 1 \pmod{4} \\ (-1)^{\alpha_j}, & p_j \cong 3 \pmod 4 \end{cases}
$$
and $$
\left( \frac{7}{p_j^{\alpha_j}} \right) \left( \frac{p_j^{\alpha_j}}{7} \right) = \begin{cases} 1^{\alpha_j} = 1 , & p_j \cong 1 \pmod{4} \\ (-1)^{\alpha_j}, & p_j = 2 \text{ or } p_j \cong 3 \pmod{4} \end{cases} \text{.}
$$ Further, a simple calculation shows $$
\left( \frac{p_j^{\alpha_j}}{3} \right) = \begin{cases} 1^{\alpha_j} = 1, & p_j \cong 1 \pmod{3} \\ (-1)^{\alpha_j}, & p_j \cong 2 \pmod{3} \end{cases}
$$ and $$
\left( \frac{p_j^{\alpha_j}}{7} \right) = \begin{cases} 1^{\alpha_j} = 1, & p_j \in \{1,2,4\} \pmod{7} \\ (-1)^{\alpha_j}, & p_j \in \{3,5,6\} \pmod{7} \end{cases}
$$ and inserting these into the above reciprocity results gives $$
\left( \frac{3}{p_j^{\alpha_j}} \right) = \begin{cases}
1 , & p_j \cong 1 \pmod{4} \text{ and } p_j \cong 1 \pmod{3} \\ (-1)^{\alpha_j}, & p_j \cong 3 \pmod{4} \text{ and } p_j \cong 1 \pmod{3} \\
(-1)^{\alpha_j} , & p_j \cong 1 \pmod{4} \text{ and } p_j \cong 2 \pmod{3} \\
(-1)^{2\alpha_j} = 1, & p_j \cong 3 \pmod{4} \text{ and } p_j \cong 2 \pmod{3}\end{cases}
$$ and $$
\left( \frac{7}{p_j^{\alpha_j}} \right) = \begin{cases}
1^{\alpha_j} = 1 , & p_j \cong 1 \pmod{4} \text{ and } p_j \in \{1,2,4\} \pmod{7} \\
(-1)^{\alpha_j}, & p_j \cong 3 \pmod{4} \text{ and} p_j \in \{1,2,4\} \pmod{7} \\
(-1)^{\alpha_j} , & p_j \cong 1 \pmod{4} \text{ and } p_j \in \{3,5,6\} \pmod{7} \\
(-1)^{2\alpha_j} = 1, & p_j \cong 3 \pmod{4} \text{ and} p_j \in \{3,5,6\} \pmod{7}
\end{cases} \text{.}
$$
Using the Chinese Remainder Theorem (of just working iteratively through small integers), we can simplify the conditions in these big blocks. $$
\left( \frac{3}{p_j^{\alpha_j}} \right) = \begin{cases}
1 , & p_j \in \{1, 11\} \pmod{12} \\
(-1)^{\alpha_j}, & p_j \in \{5, 7\} \pmod{12}
\end{cases}
$$ and $$
\left( \frac{7}{p_j^{\alpha_j}} \right) = \begin{cases}
1 , & p_j \in \{1, 3, 9, 19, 25, 27 \} \pmod{28} \\
(-1)^{\alpha_j}, & p_j \in \{5, 11, 13, 15, 17, 23 \} \pmod{28}
\end{cases} \text{.}
$$
So, for $-21 \pmod{n}$ to be a quadratic residue, $\left( \frac{-1}{p_j^{\alpha_j}} \right) \left( \frac{3}{p_j^{\alpha_j}} \right) \left( \frac{7}{p_j^{\alpha_j}} \right)$ must be $1$ for each $p_j$. This is true if exactly all or $1$ of these symbols is $1$. These are all $1$ if $p_j \in \{1, 4, 16, 25, 37, 58, 64\} \pmod{84}$. Exactly one of these symbols is $1$ if $p_j \in \{5, 11, 17, 19, 20, 23, 26, 31, 41, 44, 55, 68, 71, 76, 80\} \pmod{84}$. Discarding all the even residues (since the modulus is zero and we have resolved the contribution of the prime $2$ initially), if $p_j$ is one of these $12$ residues, $\{1, 5, 11, 17, 19, 23, 25, 31, 37, 41, 55, 71\}$ modulo $84$, $-21$ is a quadratic residue modulo $p_j$ and $-21$ is a quadratic residue modulo any product of such primes. (Note that this is very far from requiring the primes are congruent to $1$ modulo $4$.) For instance $-21 \cong 1^2 \pmod{11}$ and $-21 \cong 12^2 \pmod{55}$ are quadratic residues.
To address your first question: Suppose $x$, $y$, $a$, $b$, and $m$ satisfy $x^2 \cong a \pmod {m}$ and $y^2 \cong b \pmod {m}$. Then $\dfrac{a}{b} \cong \dfrac{x^2}{y^2} \cong x^2 y^{-2} \pmod{m}$, is a fraction that is a square modulo $m$.