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Using paths or packages is work-able. Do you see a request being made to Scripts/custom/ModTest.js?
Use Chrome to load your page, and open Developer Tools (Ctrl-SHIFT-i), in which click Network. Then refresh your page and check the url of the request to your custom module. More than likely, the url is incorrect. Correct it if possible.
I am trying to narrow down the issue whether your custom module can be located or something needs to be changed with your custom module due to the change of dojo source. JS API v3.6 is using dojo 1.8.3. Unless you have used some new dojo features that are available in dojo 1.8.5, but not 1.8.3, otherwise I would be surprised it is the code issue if works for dojo 1.8.5.
I would check the module url using Developer Tools making sure it is correct. If so, I would make some breakpoints inside the entry function of the module when it's loaded, and see which step fails.