解:(1) 把$A(-1,0),$$C(0,3)$代入$y=ax^{2}-2ax + c$得
$\begin{cases}a + 2a + c=0\\c = 3\end{cases},$
把$c = 3$代入$a + 2a + c=0$得$3a+3 = 0,$$a=-1。$
所以二次函数表达式为$y=-x^{2}+2x + 3。$
$y=-x^{2}+2x + 3=-(x - 1)^{2}+4,$所以顶点$D(1,4)。$
(2) 令$y = 0,$则$-x^{2}+2x + 3=0,$$x^{2}-2x - 3=0,$$(x - 3)(x + 1)=0,$解得$x_1 = 3,$$x_2=-1,$所以$B(3,0)。$
设直线$BC$的方程为$y=kx + d,$
把$B(3,0),$$C(0,3)$代入得$\begin{cases}3k + d=0\\d = 3\end{cases},$解得$k=-1,$$d = 3,$
$y=-x + 3。$
设$E(t,-t^{2}+2t + 3)(0<t<3),$则$F(t,-t + 3),$$EF=-t^{2}+2t + 3-(-t + 3)=-t^{2}+3t。$
$AB = 4,$$OC = 3,$$BC=\sqrt{3^{2}+3^{2}}=3\sqrt{2}。$
因为$EF// y$轴,$\angle EFC=\angle OCB。$
当$\triangle EFC\sim\triangle BCA$时,$\frac{EF}{AB}=\frac{CF}{BC},$
$CF=\sqrt{t^{2}+(-t + 3 - 3)^{2}}=\sqrt{2}t,$$\frac{-t^{2}+3t}{4}=\frac{\sqrt{2}t}{3\sqrt{2}},$$\frac{-t^{2}+3t}{4}=\frac{t}{3},$$-3t^{2}+9t = 4t,$$3t^{2}-5t = 0,$$t(3t - 5)=0,$$t=\frac{5}{3},$$EF=-(\frac{5}{3})^{2}+3\times\frac{5}{3}=\frac{20}{9}。$
当$\triangle EFC\sim\triangle BAC$时,$\frac{EF}{BC}=\frac{CF}{AB},$$\frac{-t^{2}+3t}{3\sqrt{2}}=\frac{\sqrt{2}t}{4},$$-4t^{2}+12t = 6t,$$4t^{2}-6t = 0,$$t(4t - 6)=0,$$t=\frac{3}{2},$$EF=-(\frac{3}{2})^{2}+3\times\frac{3}{2}=\frac{9}{4}。$
所以$EF=\frac{9}{4}$或$EF=\frac{20}{9}。$