So if you click a feature to open the pop-up, the pop-up doesn't open until after the layer finishes drawing? If so, then that sounds like normal behavior to me (at least it is in my experience with ExB). I think what it will come down to is improving the performance of your zoning layer.
I'm assuming your ExB app and data is all hosted in AGOL? If that's the case, you can try configuring some of the settings on the hosted feature layer (such as the spatial index and optimize layer drawing). This blog post has a lot of good information.
I don't think it would hurt to reproject the data to Web Mercator. The data essentially gets reprojected on the fly anyway when accessing it through the web map. So theoretically, it will take less processing power to display the data. But in practice, that usually happens pretty fast.
