Got your data, thanks! So I think there’s a couple issues still at play.
First, the issue I noted above – coordinates of layers appearing to be decimal degrees but the projection definition stating a UTM projection – that is an issue for the AOI and habitat shapefiles. I can see that if I look at the layer properties in QGIS, which shows me this:
CRS: EPSG:26910 - NAD83 / UTM zone 10N - Projected
Extent: -96.6394850000195333,40.3754399998292683 : -90.1400609996912863,43.5011960001858142
Those extent coordinates look like longitude/latitude decimal degrees while the CRS is suggesting they should be interpreted by software as meters. The solution is probably to redefine (not reproject) the projection definition to the correct system for those decimal degree coordinates. Or backtrack to the original datasources.
Cultivated_crop layer does not seem to have the projection problem, but it is very large and unwieldy (it has > 32 million vertices). If the original source of that layer was a raster, it is probably best to provide the raster directly to HRA instead of a vector (as of version 3.7.0, HRA can accept raster inputs).
In general, it’s always important and worthwhile to inspect all the input data in GIS before running an InVEST model. Good luck!