"getting on my nerves with the pop-up windows asking me to allow every freakin connection!"
LOL
You can turn that function on & off. I gather you didn't bother to set your LS preferences.
Anywho, to get rid of LS you could have used its uninstaller which apparently you trashed also.
+Mapping locations of where LS straggler files are.+
Home>Library>*Little Snitch<----trash this folder.*
Home>Library>Application Support>*Little Snitch<----trash this folder.*
Machintosh HD>Library>*Little Snitch<---trash this folder.*
Machintosh HD>Library>Application Support>Objective Development>*Little Snitch<----trash this folder.*
Home>Library>Preferences - *trash the following:*
at.obdev.LittleSnitchConfiguration.plist
at.obdev.LittleSnitchNetworkMonitor.plist
Empty the trash, repair permissions and restart your computer.