1. Why am I getting errors?

As a general rule, if it works in jsdoc it will work in jsdoc2md. Test your source with jsdoc -X my-code.js - if that fails it will fail in jsdoc2md too.

2. Why isn't my namepath being converted to a link?

All tags requiring a namepath argument, for example @requires module:something, should render as a link. For it to work, the namepath specified must be valid and point to an identifier in one of the files being parsed by jsdoc2md. To get a list of the valid namepaths in your sourcecode, run jsdoc2md --namepaths lib/*.js.