How to covert to (lon, lat, depth) in Tokyo Bay from (x, y, depth) with unknown (x, y) coordinates

Summary

1. Converting coastline.blz (lon, lat, z) to (utm_x, utm, y, z) creating coastline.xyz using Proj
2. Adjusting dep.xyz, (x, y, depth), to coastline.xyz by parallel shifting with trial and error manner using GMT and creating dep_utm.xyz
3. Converting dep_utm.xyz to dep.blz (lon, lat, depth) using Proj

UTM grid zones is here. Zone 54N covers Tokyo Bay and Tohoku District.

Converting lon-lat to XY using Proj to generate mesh for FVCOM

# Set the zone number (see http://www.dmap.co.uk/utmworld.htm)
zone=54
inf=coastline.blz
proj +proj=utm +zone=$zone +ellps=WGS84 +datum=WGS84 +units=m +no_defs $inf

The format of coastline.blz:

# -b
101.033012    -3.999887   0.0
101.031252    -4.001647   0.0
101.031252    -4.002527   0.0
101.030372    -4.003407   0.0