In the experiment you are finding the angular velocity needed to create a force on $W_1$ of magnitude $W_2g$ (where $g$ is the acceleration due to gravity). For an object moving in a circle of radius $r$ and angular velocity $\omega$ the acceleration is given by $a = r\omega^2$ so the force is $F = W_2g = W_1r\omega^2$. Since you're keeping the force constant, you can rearrange the equation to give:
$$ r = \frac{W_2g}{W_1} \frac{1}{\omega^2} = \frac{W_2g}{W_1} \frac{\tau^2}{4\pi^2} $$
where $\tau$ is the period and I've used the equation $\omega = 2\pi/\tau$. So $r$ is proportional to $\tau^2$ and a graph of $r$ against $\tau^2$ should give a straight line.
Now you can probably see why in the second experiment you graph $W_2$ against $\tau^{-2}$. If you take the equation above and rearrange it to get $W_2$ as a function of $\omega$ you get:
$$ W_2 = \frac{W_1r}{g} \omega^2 = \frac{W_1r}{g} \frac{4\pi^2}{\tau^2} $$
so $W_2$ is proportional to $\tau^{-2}$.
Response to comment:
The acceleration is given by $a = r\omega^2$ where $\omega$ is the angular velocity. $\omega$ is related to the tangential velocity $v$ by $\omega = v/r$. If you substitute for $\omega$ in the expression for the acceleration you get:
$$ a = r\omega^2 = r \left( \frac{v}{r} \right)^2 = \frac{v^2}{r}$$
So you are quite correct that $a = v^2/r$.
Response to response to comment
If you take my first equation and rearrange it to get $\tau^2$ in terms of $r$ you get:
$$ \tau^2 = \frac{4\pi^2 W_1}{W_2 g} r $$
so if you graph $\tau^2$ against $r$ the gradient will be $(4\pi^2 W_1)/(W_2 g)$. This is the same result as in the Google doc, $m(2\pi N)^2/F_c$, but that document uses $m$ to denote $W_1$ and $F_c$ for $W_2g$. Also the period I've used, $\tau$, is the period for one revolution so in their equation $N$ is one.
When you're doing the calculation it's certainly easiest to use SI units from the beginning so you don't make a mistake with units along the way. If you want to put your experimental data into a Google docs spreadsheet I'd be happy to have a look at it. Remember to include the values for $W_1$ and $W_2$ as well as the values for $r$ and $\tau$ (remember to say how many revolutions you timed).