The $2D$ case is not a problem:
$$\ P(t) =(x,y)= s + t v = <s_x+tv_x, s_y+tv_y> $$
$$\ F(x,y) = (\frac{x}{a})^2 +(\frac{y}{b})^2 -1 = 0 $$ $$ \nabla F(x,y).v =0 $$
Finally solve for $y$ in terms of $x$, and plug into ellipse equation, $F(x,y)$.
For the $3D$ case, where I have $P(t)= (x,y,z)$ and am now using a $3D$ ellipsoid, the previous method does not work. I am left with more variables than equations. Any advice is appreciated.
$$\ P(t) =(x,y,z)= s + t v = <s_x+tv_x, s_y+tv_y, s_z+tv_z> $$
$$\ F(x,y,z) = (\frac{x}{a})^2 +(\frac{y}{b})^2 +(\frac{z}{c})^2-1 = 0 $$
EDIT: Thank you for the feedback.
@ja72: Your solution has been tested and works.
@Semiclassical: I have been looking at Lagrange Multipliers and have an idea for how to solve my problem. The steps below have been tested and work.
(1) Given a line defined by two points $\vec{x1}$ and $\vec{x2}$, $\vec{r}$ , I know the equation for the minimum distance between $\vec{r}$ and a point $\vec{x0}$ $$\ d(x_0,y_0,z_0) = \frac{|(\vec{x0}-\vec{x1})X(\vec{x0}-\vec{x2})|}{|\vec{x2}-\vec{x1}|} $$
(2) Given my constraint that the point $\vec{x0}$ must reside on the ellipse $$\ F(x_0,y_0,z_0) = (\frac{x_0}{a})^2 +(\frac{y_0}{b})^2 +(\frac{z_0}{c})^2-1 = 0 $$
(3) The Lagrange problem is stated below and is solved by following (http://tutorial.math.lamar.edu/Classes/CalcIII/LagrangeMultipliers.aspx):
Find the minimum of $\ d(x_0,y_0,z_0) $ subject to the constraint $\ F(x_0,y_0,z_0) $.

Appendix
The 6 Plüker coordinates of a line through points $\vec{r}_1$ and $\vec{r}_2$ are $$ L = (\vec{r}_2-\vec{r}_1, \, \vec{r}_1 \times \vec{r}_2 ) $$