I'm not sure if this is true, but it seems like the path to FiScript is hardcoded to /Applications/FiScript.app/Contents/PlugIns/FiScriptHelper.app.
Here's the error message:
Can't communicate with helper application.
Check if Helper applications exists at /Applications/FiScript.app/Contents/PlugIns/FiScriptHelper.app Helper application has been moved or deleted. Please move the helper application back or reinstall FiScript.
This is a problem, because by default I set Homebrew to install everything in ~/Applications/.