Should we have a unique module name per .ts file
Yes use amd/commonjs : https://www.youtube.com/watch?v=KDrWLMUY0R0&hd=1
per folder
Yes create an index.js
that exports everything from a folder.
When a class is dependent on other classes, should we wrap that .ts file in a require/define (we use require.js) for the dependencies?
no. Use the built in import
statement in TypeScript
We are having to put in a ton of /// statements. Is there a way to have global ones?
Yes look at reference files
https://github.com/grunt-ts/grunt-ts#reference-file-generation
Any other suggestions for what we should and should not do for a project this large?
Depend on TypeScript as much as you can and then refactoring to a different pattern will not be too hard when one emerges (you should get compile errors)