I will give an elementary proof of the problem using the fact, that $T^2$ is a topological group and that its universal cover is contractible. We will start with some constructions in homotopy theory of topological groups, which are required to understand the proof given below and added here for convenience.
First note, that $\mathbb R^2$ forms a topological group under addition: $(x,y) + (x',y') := (x+x',y+y')$ and that $\mathbb Z^2$ is a discrete normal subgroup thereof. We identify $T^2$ with the quotient of $\mathbb R^2$ by $\mathbb Z^2$, so that $T^2$ again becomes a topological group under addition. Moreover the quotient map $p: \mathbb R^2 \to T^2$ becomes a group homomorphism and is easily seen to be the universal covering projection ($\mathbb Z^2$ discrete subgroup $\Rightarrow$ $p$ is covering projection; $\mathbb R^2$ is contractible $\Rightarrow$ $p$ is universal).
Next, we observe, that for $[f],[g]\in [(X,\ast),(T^2,0)]$ the sum $[f]+[g] := [f+g]$ is well defined, turning $[(X,\ast),(T^2,0)]$ into a group. The same arguments show that $[(X,\ast),(\mathbb R^2,0)]$ is a group under point wise addition of representatives as well (as is $[(X,\ast),(G,1)]$ for any topological group $G$ with unit $1$), and that the map $p_\sharp : [(X,\ast),(\mathbb R^2,0)] \to [(X,\ast),(T^2,0)]$ given by $p_\sharp([f]) := [p \circ f]$ is a group homomorphism.
Now $\pi_1(T^2,0) = [(S^1,1), (T^2,0)]$ is a group in two ways, by means of composition of (representatives of) loops $[\alpha], [\beta] \mapsto [\alpha \ast \beta]$ and by means of point wise addition of (representatives of) loops $[\alpha], [\beta] \mapsto [\alpha + \beta]$.
Both operations share the same unit, the (class of the) constant loop sending everything to $0 \in T^2$ and denoted simply by $0: (S^1,1) \to (T^2,0)$. We can also observe, that for any loops $\alpha, \beta, \gamma, \delta$ we have $(\alpha + \beta) \ast (\gamma + \delta) = (\alpha + \gamma) \ast (\beta + \delta)$. Therefore $$[\alpha]+[\beta] = ([\alpha] \ast [0]) + ([0] \ast [\beta]) = ([\alpha] + [0]) \ast ([0] + [\beta]) = [\alpha] \ast [\beta],$$
hence the two operations are in fact the same on $\pi_1(T_2,0)$. The same argument can be used to show the analogous statement for $\pi_1(\mathbb R^2,0)$ (or $\pi_1(G,1)$ for any topological group $G$ with unit $1$).
Now back to the problem:
Given two maps $\varphi, \psi: T^2 \to T^2$, such that for some point $x \in T^2$, we have $\varphi(x) = \psi(x) = x$ and $\pi_1(\varphi) = \pi_1(\psi): \pi_1(T^2,x) \to \pi_1(T^2,x)$, we want to show $\varphi \simeq \psi$, where the homotopy can be taken relative to $x$. Replacing $\varphi$ with $\xi \mapsto \varphi(\xi + x) - x$ and $\psi$ with $\xi \mapsto \psi(\xi + x) - x$ if necessary, we may assume $x=0$. It will then suffice to show, that $\chi \simeq 0$, where $\chi := \varphi - \psi$.
Since the induced map $\pi_1(\chi): \pi_1(T^2,0) \to \pi_1(T^2,0)$ on fundamental groups is trivial (this is where we need all the constructions for topological groups), we can lift $\chi$ to a map $\bar{\chi}: (T^2,0) \to (\mathbb R^2,0)$ with $\chi = p \circ \bar{\chi}$.
We now define $H: T^2 \times I \to T^2$ by $H(x,t) = p(t\bar\chi(x))$, which is easily checked to be the required homotopy $0 \simeq \chi$.
Best Answer
To answer the question in the title: no, of course not, different maps into a path-connected space are not necessarily homotopic. A space $X$ such that for all spaces $Y$, all maps $f,g Y \to X$ are homotopic is either contractible or empty. Indeed, if $X$ is nonempty, choose $Y = X$, $f = \operatorname{id}_X$ and $g$ a constant map; then the identity is homotopic to a constant map so by definition $X$ is contractible.
It is true that for all values of $x$, you can construct a path between $f(x)$ and $g(x)$; but it's not necessarily possible to choose such a homotopy continuously. If the map is not nullhomotopic then at some point there will be some kind of tearing, and the resulting map will not be continuous.
To answer the question in the body: there is a simplicial complex structure on $S^k$ with exactly two cells, one in dimension $0$ and one in dimension $k$. So if $f : S^m \to S^n$ is a map, $m < n$, by the simplicial approximation theorem $f$ is homotopic to a map $g : S^m \to S^n$ such that the image of the $m$-skeleton of $S^m$ is included in the $m$-skeleton of $S^n$. But the $m$-skeleton of $S^m$ is $S^m$, whereas the $m$-skeleton of $S^n$ is a point ($m < n$). It follows that $f$ is homotopic to a constant map.