Percentage difference between two signals
At the least you should normalize it by the length of the sequence. But what you're trying to do is a pretty standard thing. I'm not sure what percentage difference really means. What you should probably be using is something like the root mean squared error:

$$RMSE=\sqrt{\frac{1}{N}\sum_{n=0}^{N-1}(x(n)-y(n))^2}$$

where $x(n)$ and $y(n)$ are your two sequences.