【解析】(1)依题意有 $A=1$ ,则 $f(x)=\sin (x+\varphi)$ ,
将点 $M\left(\frac{\pi}{3}, \frac{1}{2}\right)$ 代入得 $\sin \left(\frac{\pi}{3}+\varphi\right)=\frac{1}{2}$ ,
而 $0<\varphi<\pi, \quad \therefore \frac{\pi}{3}+\varphi=\frac{5}{6} \pi, \quad \therefore \varphi=\frac{\pi}{2}$ ,
故 $f(x)=\sin \left(x+\frac{\pi}{2}\right)=\cos x$ ;
> (2)依题意有 $\cos \alpha=\frac{3}{5}, \cos \beta=\frac{12}{13}$ ,而 $\alpha, \beta \in\left(0, \frac{\pi}{2}\right)$ ,
$$
\begin{aligned}
& \therefore \sin \alpha=\sqrt{1-\left(\frac{3}{5}\right)^{2}}=\frac{4}{5}, \sin \beta=\sqrt{1-\left(\frac{12}{13}\right)^{2}}=\frac{5}{13} \\
& \quad f(\alpha-\beta)=\cos (\alpha-\beta)=\cos \alpha \cos \beta+\sin \alpha \sin \beta=\frac{3}{5} \times \frac{12}{13}+\frac{4}{5} \times \frac{5}{13}=\frac{56}{65}
\end{aligned}
$$