diff --git a/src/spinup_evaluation/cli.py b/src/spinup_evaluation/cli.py
index d430124..203c201 100644
--- a/src/spinup_evaluation/cli.py
+++ b/src/spinup_evaluation/cli.py
@@ -145,7 +145,7 @@ def apply_metrics_restart(data: xr.Dataset, mask: xr.Dataset) -> Dict[str, Any]:
         ),
         # Name suggests temperature, but kept as-is from original code.
         "temperature_DWbox_metric": lambda d: temperature_DWbox_metric(
-            d["velocity_u"][0], mask
+            d["temperature"][0], mask
         ),
         "ACC_Drake_metric": lambda d: ACC_Drake_metric(d["velocity_u"][0], mask),
         "ACC_Drake_metric_2": lambda d: ACC_Drake_metric_2(
@@ -187,7 +187,7 @@ def apply_metrics_output(
         ),
         # Name suggests temperature, but kept aligned with original mapping:
         "temperature_DWbox_metric": lambda: temperature_DWbox_metric(
-            grid_output["velocity_u"], mask
+            grid_output["temperature"], mask
         ),
         "ACC_Drake_metric": lambda: ACC_Drake_metric(grid_output["velocity_u"], mask),
         "ACC_Drake_metric_2": lambda: ACC_Drake_metric_2(
diff --git a/src/spinup_evaluation/loader.py b/src/spinup_evaluation/loader.py
index 1fa6a24..511f168 100644
--- a/src/spinup_evaluation/loader.py
+++ b/src/spinup_evaluation/loader.py
@@ -2,6 +2,7 @@
 
 import glob
 import os
+from pathlib import Path
 from typing import Dict, Mapping, Optional, Union
 
 import xarray as xr
@@ -120,8 +121,26 @@ def _normalise_var_specs(
     return normalised
 
 
-def load_mesh_mask(path: str) -> xr.Dataset:
+def resolve_mesh_mask(mesh_mask: str, sim_path: str) -> Path:
+    """Resolve the mesh mask path, handling absolute and relative paths."""
+    p = Path(mesh_mask)
+    candidate = p if p.is_absolute() else Path(sim_path) / mesh_mask
+    if not candidate.exists():
+        hint = (
+            "Set `mesh_mask` to an absolute path in your YAML, "
+            "or ensure it exists under --sim-path."
+        )
+        msg = f"Mesh mask file not found: {candidate}. {hint}"
+        raise FileNotFoundError(msg)
+
+    return candidate
+
+
+def load_mesh_mask(path: Path) -> xr.Dataset:
     """Load the NEMO mesh mask file and validate required fields."""
+    if not path.exists():
+        msg = f"Mesh mask file not found: {path}"
+        raise FileNotFoundError(msg)
     ds = xr.open_dataset(path)
     required_vars = ["tmask", "e1t", "e2t", "e3t_0"]
     missing = [v for v in required_vars if v not in ds.variables]
@@ -237,7 +256,10 @@ def load_dino_data(
     if "mesh_mask" not in setup:
         msg = "setup must specify 'mesh_mask'."
         raise ValueError(msg)
-    mesh_mask_path = os.path.join(base, str(setup["mesh_mask"]))
+
+    # Resolve mesh mask path
+    mesh_mask_path = resolve_mesh_mask(str(setup["mesh_mask"]), base)
+
     data["mesh_mask"] = load_mesh_mask(mesh_mask_path)
 
     # restart (optional / controlled by mode)
diff --git a/src/spinup_evaluation/metrics.py b/src/spinup_evaluation/metrics.py
index 14534fc..45c234f 100644
--- a/src/spinup_evaluation/metrics.py
+++ b/src/spinup_evaluation/metrics.py
@@ -31,7 +31,7 @@ def check_density(density: xarray.DataArray, epsilon: float = 1e-5):
     """
     density = density.where(density != 0)
     diff = density - density.shift(depth=-1)
-    bad_prop = (diff > epsilon).mean(dim=["depth", "nav_lat", "nav_lon"])
+    bad_prop = (diff > epsilon).mean(dim=["depth", "y", "x"])
     return bad_prop
 
 
@@ -81,9 +81,9 @@ def temperature_500m_30NS_metric(
     )
 
     # Returning Average Temperature at 500m depth as a numpy scalar
-    return (t500_30NS * area_500m_30NS).sum(
-        dim=["nav_lat", "nav_lon"]
-    ) / area_500m_30NS.sum(dim=["nav_lat", "nav_lon"])
+    return (t500_30NS * area_500m_30NS).sum(dim=["y", "x"]) / area_500m_30NS.sum(
+        dim=["y", "x"]
+    )
 
 
 def temperature_BWbox_metric(temperature: xarray.DataArray, file_mask: xarray.Dataset):
@@ -140,10 +140,9 @@ def temperature_BWbox_metric(temperature: xarray.DataArray, file_mask: xarray.Da
             * (abs(temperature.nav_lat) < LAT_BOUND)
         )
     )
-
     # Returning Average Temperature on Box
-    return (t_BW * area_BW).sum(dim=["nav_lat", "nav_lon", "depth"]) / area_BW.sum(
-        dim=["nav_lat", "nav_lon", "depth"]
+    return (t_BW * area_BW).sum(dim=["y", "x", "depth"]) / area_BW.sum(
+        dim=["y", "x", "depth"]
     )
 
 
@@ -203,9 +202,10 @@ def temperature_DWbox_metric(temperature: xarray.DataArray, file_mask: xarray.Da
         )
     )
 
+    breakpoint()
     # Returning Average Temperature on Box
-    return (t_DW * area_DW).sum(dim=["nav_lat", "nav_lon", "depth"]) / area_DW.sum(
-        dim=["nav_lat", "nav_lon", "depth"]
+    return (t_DW * area_DW).sum(dim=["y", "x", "depth"]) / area_DW.sum(
+        dim=["y", "x", "depth"]
     )
 
 
@@ -235,20 +235,20 @@ def ACC_Drake_metric(uo, file_mask):
         1D DataArray (over time_counter), representing the total transport across Drake
         Passage (in Sv). Length is 1 if only a single time step is present.
     """
-    umask_Drake = file_mask.umask.isel(nav_lon=0).squeeze()
+    umask_Drake = file_mask.umask.isel(x=0).squeeze()
     e3u = file_mask.e3u_0.squeeze()
     e2u = file_mask.e2u.squeeze()
 
     # Masking the variables onto the Drake Passage
 
-    u_masked = uo.isel(nav_lon=0) * umask_Drake
-    e3u_masked = e3u.isel(nav_lon=0) * umask_Drake
-    e2u_masked = e2u.isel(nav_lon=0) * umask_Drake
+    u_masked = uo.isel(x=0) * umask_Drake
+    e3u_masked = e3u.isel(x=0) * umask_Drake
+    e2u_masked = e2u.isel(x=0) * umask_Drake
 
     # Multiplying zonal velocity by the sectional areas (e2u*e3u)
 
     ubar = u_masked * e3u_masked
-    flux = (e2u_masked * ubar).sum(dim=["nav_lat", "depth"])
+    flux = (e2u_masked * ubar).sum(dim=["y", "depth"])
     # Returning Total Transport across Drake passage as a numpy scalar (unit : Sv)
     return flux / 1e6
 
@@ -283,22 +283,22 @@ def ACC_Drake_metric_2(
         1D DataArray (over time_counter), representing the total transport across Drake
         Passage (in Sv). Length is 1 if only a single time step is present.
     """
-    umask_Drake = file_mask.umask.isel(nav_lon=0).squeeze()
+    umask_Drake = file_mask.umask.isel(x=0).squeeze()
     e3u_0 = file_mask.e3u_0.squeeze()
     e2u = file_mask.e2u.squeeze()
 
     # Recomputing e3u, using ssh to refactor the original e3u_0 cell heights)
-    ssh_u = (ssh + ssh.roll(nav_lon=-1)) / 2
+    ssh_u = (ssh + ssh.roll(x=-1)) / 2
     bathy_u = e3u_0.sum(dim="depth")
     ssumask = umask_Drake[:, 0]
     e3u = e3u_0 * (1 + ssh_u * ssumask / (bathy_u + 1 - ssumask))
     # Masking the variables onto the Drake Passage
-    u_masked = uo.isel(nav_lon=0) * umask_Drake
-    e3u_masked = e3u.isel(nav_lon=0) * umask_Drake
-    e2u_masked = e2u.isel(nav_lon=0) * umask_Drake
+    u_masked = uo.isel(x=0) * umask_Drake
+    e3u_masked = e3u.isel(x=0) * umask_Drake
+    e2u_masked = e2u.isel(x=0) * umask_Drake
     # Multiplying zonal velocity by the sectional areas (e2u*e3u)
     ubar = u_masked * e3u_masked
-    flux = (e2u_masked * ubar).sum(dim=["nav_lat", "depth"])
+    flux = (e2u_masked * ubar).sum(dim=["y", "depth"])
     # Return Total Transport across Drake passage as a numpy scalar (unit : Sv)
     return flux / 1e6
 
@@ -335,7 +335,7 @@ def NASTG_BSF_max(
     e1v = file_mask.e1v.squeeze()
     vmask = file_mask.vmask.squeeze()
     # Updating e3v from e3v_0 and SSH
-    ssh_v = (ssh + ssh.roll(nav_lat=-1)) / 2
+    ssh_v = (ssh + ssh.roll(y=-1)) / 2
     bathy_v = e3v_0.sum(dim="depth")
     ssvmask = vmask.isel(depth=0)
     e3v = e3v_0 * (1 + ssh_v * ssvmask / (bathy_v + 1 - ssvmask))
@@ -346,12 +346,13 @@ def NASTG_BSF_max(
     # (BSF=0)
     V = (vo * e3v).sum(dim="depth")  #  == "Barotropic Velocity" * Bathymetry
     BSF = (V * e1v * ssvmask).cumsum(
-        dim="nav_lon"
+        dim="x"
     ) / 1e6  # Integrating from the West, and converting from m³/s to Sv
     # Selecting 0N-40N window where to search for the maximum, which will correspond to
     # the center of rotation for the gyre
-    BSF_NASPG = BSF.where(abs(BSF.nav_lat - 20) < 20)  # noqa: PLR2004
+    breakpoint()
+    BSF_NASPG = BSF.where(abs(vo.nav_lat - 20) < 20)  # noqa: PLR2004
 
     # Selecting the maximum value of the BSF in the selected window
     # and return it as a numpy scalar
-    return BSF_NASPG.max(dim=["nav_lat", "nav_lon"])
+    return BSF_NASPG.max(dim=["y", "x"])
diff --git a/src/spinup_evaluation/standardise_inputs.py b/src/spinup_evaluation/standardise_inputs.py
index bdf5961..6d581be 100644
--- a/src/spinup_evaluation/standardise_inputs.py
+++ b/src/spinup_evaluation/standardise_inputs.py
@@ -29,8 +29,8 @@
         "depthu",
         "depthv",
     ],  # Depth can be 'depth', 'nav_lev', or 'deptht'
-    "latitude": ["nav_lat", "y"],  # Latitude can be 'nav_lat' or 'y'
-    "longitude": ["nav_lon", "x"],  # Longitude can be 'nav_lon' or 'x'
+    # "latitude": ["nav_lat", "y"],  # Latitude can be 'nav_lat' or 'y'
+    # "longitude": ["nav_lon", "x"],  # Longitude can be 'nav_lon' or 'x'
     "ssh": ["sshn", "ssh"],  # Sea surface height could be 'sshn' or 'ssh'
     "time_counter": [
         "time_counter",
@@ -72,14 +72,23 @@ def standardise(dataset, variable_dict):
                 break
 
     ds = ds.rename(rename_map)
+    breakpoint()
 
-    if "x" in ds.dims:
-        ds = ds.rename({"x": "nav_lon"})
-    if "y" in ds.dims:
-        ds = ds.rename({"y": "nav_lat"})
+    # if "x" in ds.dims:
+    #     ds = ds.rename({"x": "nav_lon"})
+    # if "y" in ds.dims:
+    #     ds = ds.rename({"y": "nav_lat"})
+
+    # Promote nav_lat and nav_lon to coordinates if they are not already
+    # Error is exhibited in DINO restart file
+    for name in ("nav_lat", "nav_lon"):
+        if name in ds and name not in ds.coords:
+            ds = ds.set_coords(name)  # zero-copy promotion to coordinate
 
     if is_da:
         new_name = rename_map.get(orig_name, orig_name)
         return ds[new_name]
 
+    # breakpoint()
+
     return ds