3. $P_{k-1}(t,d)$ divides $A+ P_{k-2}(t,d)d \,I $$A+ P_{k-2}(t,d)d I $
Conversely, if $(d,t)$ satisfy (1,2,3), there exists a $B\in M_2 (\mathbb Z)$ with characteristic polynomial $z^2-tz+d$. Precisely, if $P_{k-1}(t,d)\ne0$, it is unique, namely $$B:=\frac1{P_{k-1}(t,d)}\Big(A+ P_{k-2}(t,d)d \,I \Big).$$$$B:=\frac1{P_{k-1}(t,d)}\Big(A+ P_{k-2}(t,d)d I \Big).$$ If $P_{k-1}(t,d)=0$, then $A=mI$, is an integer multiple of the identity, and all the infinitely many $B\in M_2 (\mathbb Z)$ with with characteristic polynomial $z^2-tz+d$ satisfy $B^k=A$.
Proof. Assume $A=B^k$ and $B\in M_2 (\mathbb Z)$ and set $t:=\text{tr}(B)$ and $d:=\det(B)$. Then (1) is $\det(A)=\det(B^k)=\det(B)^k=p^k$. As seen above, the characteristic polynomial of $B$, $p_B(z):=z^2-tz+d $ divides the polynomial $z^k-P_{k-1}(t,d)z+P_{k-2}(t,d)d$, and since by Cayley-Hamilton $B^2-tB+d=0$, we also have $$B^k-P_{k-1}(t,d)B+P_{k-2}(t,d)d\, I=0,$$$$B^k-P_{k-1}(t,d)B+P_{k-2}(t,d)d I=0,$$ so, taking the trace, we have $\text{tr}(A)= P_{k-1}(t,d)t -2P_{k-2}(t,d)d$, which is (2), while $P_{k-1}(t,d)B= A+P_{k-2}(t,d)d\, I$$P_{k-1}(t,d)B= A+P_{k-2}(t,d)d I$, is (3).
Conversely, assume the above conditions (1,2,3) hold for integers $t,d$. Consider first the case $P_{k-1}(t,d)\ne0$. So one can define $$B:=\frac1{P_{k-1}(t,d)}\Big(A+ P_{k-2}(t,d)d \,I \Big),$$$$B:=\frac1{P_{k-1}(t,d)}\Big(A+ P_{k-2}(t,d)d I \Big),$$ an element of $M_2 (\mathbb Z)$ thanks to (3). The trace and determinant of $B$ are then by (1,2), hidding the variables $(t,d)$ in the $P_j$ $$\text{tr}(B)=\frac{\text{tr}(A)+ 2P_{k-2}d}{P_{k-1} } = \frac{P_k +P_{k-2} d }{P_{k-1} } =\frac{ t P_{k-1} }{P_{k-1} } =t $$ $$\det(B)= \frac{\det\Big(A+ P_{k-2} d \,I \Big)}{P_{k-1} ^2} = \frac{P_{k-2}^2d^2 + \text{tr}(A)P_{k-2} d +\det(A) }{P_{k-1}^2}=$$$$\det(B)= \frac{\det\Big(A+ P_{k-2} d I \Big)}{P_{k-1} ^2} = \frac{P_{k-2}^2d^2 + \text{tr}(A)P_{k-2} d +\det(A) }{P_{k-1}^2}=$$ $$=\frac{P_{k-2}^2d^2 + \big(P_k-P_{k-2}d\big)P_{k-2}d +d^k }{P_{k-1}^2}= $$ $$=\frac{ P_kP_{k-2}d +d^k }{P_{k-1}^2}= d,$$ because $P_{k-1}^2 -P_kP_{k-2} =d^{k-1}$. Thus the characteristic polynomial of $B$ is $z^2-tz+d$, which implies $B^k=P_{k-1}B-P_{k-2}d\, I=A$. Finally, consider the case $P_{k-1}(t,d)=0$. By (3) $A$ is then a multiple of the identity, $A=m\, I$$A=m I$, for $m:=-P_{k-2}(t,d)d$. If $m=0$, any nilpotent $B$ has the wanted properties. If $m\ne 0$, let $\lambda$ and $\mu$ be the roots of $z^2-tz+d$, so $t=\lambda+\mu$ and $d=\lambda\mu$. Then we have $\lambda\neq\mu$, otherwise $0=P_{k-1}(\lambda+\mu,\lambda\mu)=k\lambda^{k-1}$ and $\lambda=\mu=0=t=d$ and $A=0$. Also (see below) $$0= P_{k-1}(\lambda+\mu,\lambda\mu)= \frac{\lambda^k-\mu^k}{\lambda-\mu} $$ whence $\lambda^k=\mu^k$, and $$m =-\lambda\mu P_{k-2}(\lambda+\mu,\lambda\mu)=-\frac{\lambda^k\mu-\mu^k\lambda}{\lambda-\mu} = \lambda^k=\mu^k.$$ Let $B$ one of the infinitely many matrices in $M_2 (\mathbb Z)$ with characteristic polynomial $z^2-tz+d$. Since $\lambda\ne \mu$, $B$ is diagonalizable, $B=Q^{-1}\text{diag}(\lambda,\mu)Q$, so $$B^k=Q^{-1}\text{diag}(\lambda^k,\mu^k)Q=Q^{-1}mIQ=mI=A,$$ ending the proof.