Thank you for your input, this helped solve my issue. One thing that is lost with Feature Servers is the ability to have layers grouped, which is a pretty big deal for me. I want both the ability to have layers grouped in the layer list AND the ability to highlight a selected feature. I was able to get around this by doing the following:
1. Publish both a MapServer and a FeatureServer out to Server
2. Author an ArcGIS.com web map by importing the MapServer (this allows you to have grouped layers in your layer list)
3. Reference that maps 'ID' number in your JS API code under "portal item"
4. For each layer that you want to be highlighted when selected manual add them to your webmap using the FeatureServer REST url in your code using the "FeatureLayer" class from the API.
5. When creating the FeatureLayer in step 4, set the property 'listMode" to 'hide' and 'legendEnabled' to false....this will prevent the layer from showing up in the layer list and legend, as you are only adding it to the map so the .hitTest() function will have something to interact with. You don't actually need to see this on the map/in the layer list or legend as it is a duplicate of the layer that is already present in the MapServer added in step 2.
6. Use the JS code in this topic to set up the function to highlight the graphics layer
This will give you the best of both worlds if you want to be able to both highlight any features selected AND still use a MapService to allow grouped layers.