How do I measure the voltage across R3 (Va) in this circuit?
In your initial equation (which appears to be KCL applied at the "center" node), there are a couple of errors.

A couple of important distinctions:


Node voltages are different than element voltages.  \$V_A\$ is an element voltage (its + and - are placed across an element).  The center node has a potential (voltage) with respect to ground, I'll call it \$V_{center}\$.  It is very unlikely that \$V_A = V_{center}\$.
Sources do not obey Ohm's Law.  It doesn't matter if they are independent or dependent or current or voltage.  When writing KCL at a node connected to a current source, that source's current is what you should write in your equation.


With these comments, I would write your first equation as

\$ \frac{5-V_{center}}{R_1} - \frac{V_{center} - V_{right}}{R_3} - i_1 = 0, \$

where I've named the node between \$R_3\$ and \$R_4\$ "right".

There's more to do, but I hope this points you in a more profitable direction.