It seems I was confused or made mistakes the first time trying to solve this, so I will post my solution now that it makes sense.
Assume $u(x,t)=F(x+2t)+G(x-2t)$. Then, the initial conditions give us:
$$
u(x,0)=F(x)+G(x)=e^{-x}\\
u_t(x,0)=2F'(x)-2G'(x)=2e^{-x}
$$
which hold for all $x>0$.
Hence, in the last equation, we may divide both sides by 2 and integrate with respect to x, then solve the resulting system:
$$
\begin{cases}
F(x)+G(x)=e^{-x}\\
F(x)-G(x)=-e^{-x}+C
\end{cases}
$$
where $C$ is some constant.
We thus obtain $F(x)=C/2$ and $G(x)=e^{-x}-C/2$. Since the only condition is that $x$ is positive, we may replace it by any positive quantity (I think this is where I was previously confused). Thus, we obtain $u(x,t)=F(x+2t)+G(x-2t)=C/2+e^{-(x-2t)}-C/2=e^{2t-x}$ which holds for all $x>2t$. It is clear, as I noted in my original post, that this corresponds to the same solution that we get from d'Alembert's formula.
Now we handle the case when the argument to $G$ is negative. For this, we need to use the boundary condition.
We have $u_x(0,t)=F'(2t)+G'(-2t)=-\cos t$ for all $t>0$. Make the substitution $z=-2t$ to obtain $G'(z)=-\cos(z/2)-F'(-z)=-\cos(z/2)$ by noting that $F'(-z)=0$ from our previous work. Integrating, we obtain $G(z)=-2\sin(z/2)+\tilde{C}$.
Applying the continuity condition, we must have $G(0)=\tilde{C}=1-C/2$. Thus, we have $u(x,t)=F(x+2t)+G(x-2t)=1-2\sin(x/2-t)$ for $0<x<2t$.
Hence, the complete solution is:
$$u(x,t)=\begin{cases}1-2\sin(x/2-t),&0<x\leq 2t\\e^{2t-x},&x>2t\end{cases}.$$
We can now verify that the initial conditions, boundary condition, and continuity are satisfied.
Best Answer
Have you thought of using spatial Fourier series? Using the spatial periodicity hypothesis, we may expand $$u(x,t) =\sum_n a_n(t)\cos (nkx) + b_n(t)\sin (nkx)$$ as a spatial Fourier series with period $2\pi/k$. The PDE $u_{tt}=u_{xx}$ leads to a set of second-order ODEs for $a_n$, $b_n$, while the initial conditions of the PDE give the initial conditions $a_n(0)$, $b_n(0)$, $a'_n(0)$, $b'_n(0)$ of the ODEs.
Alternatively, using the method of characteristics, one may be able to develop a modified d'Alembert formula (see chap. 12-* of the book (1)).
(1) R. Habermann, Applied Partial Differential Equations; with Fourier Series and Boundary Value Problems, 5th ed., Pearson Education Inc., 2013.