This should be posted in the Haas Lathes Forum.
Check setting 64, it should be off. If all of the tools are set from a common point in Z, then your work offset is the distance from that point to the face of the part. So, if you have touched all tools to the face of the chuck, then your G54 would equal the distance from the face of the chuck to the end of the part (positive value).
Your tool calls in the NC example are correct.