When you execute 'npm install flot' what you should find is in the folder where you executed that command is a node_modules folder under which should be a folder called 'flot'. Here is where all of the packaged distributed files will be unpacked to. Any examples you created would need to reference the files here. You can either reference the full set of functionality using the minified single 'jquery.flot.js' file in the 'dist' folder, or reference individual files located under the 'source' folder.
View the source of this example
to see how it includes the scripts (it uses the unminified scripts from the 'source' folder).
Regarding the legends, they almost certainly have changed quite a bit from the 0.8.3 release and I'd be happy to help with trying to move you to the newer versions as well as identifying the functional gaps so we can create Issues to track them.