My final solution was to re-download the data sets and all my alignment issues were solved.
I am working on a personal project overlaying the location of churches/parishes on various counties in New Jersey. The parishes are contained in a .geojson file and the state counties come from a shapefile provided by the state.
When both layers are loaded the parish layer is way up to the left of the counties and both have different CRSs. The parish is EPSG:4326 - WGS 84 while the counties are the same as the project crs EPSG:3857 - WGS 84 / Pseudo Mercator. When I change the crs of the parish layer to the projects there are alignment issues and scale issues. The parishes are much closer (but still not over the counties) and to the bottom left. Further the scaling goes wrong and all the data points are much to close to each other.
How do I resolve this alignment issue?
The final result is I will be making a map to print out, which I can do now my manual exporting the layers at a fixed scale. Then I can manually align the two exports in my image editing software. I would prefer to figure out this issue mainly to learn more about these things.
Key Information and Links:
Parish Layer CRS: EPSG:4326 - WGS 84
Project CRS: EPSG:3857 - WGS 84 / Pseudo Mercator
Base data source comes from State of New Jersey - GIS Open Data State Counties.
Link Here: https://njogis-newjersey.opendata.arcgis.com/datasets/5f45e1ece6e14ef5866974a7b57d3b95_1/geoservice?geometry=-78.816%2C39.583%2C-70.472%2C41.049
I made the parish data source using geojson.io. You can view the data source one either:
GitHub: https://github.com/pulsence/diocese-of-metuchen-parish-map or
I am using for this project QGIS 3.0.3-Girona.