As I see them ,here are the Z moves in your file. Since you are setting G90, all moves are absolute from Z0:

in line 7, Z rises to 1"
in line 8, Z lowers to .045"
in line 267, Z lowers to .063"
in line 526, Z again rises to 1"
in line 528, Z again lowers to .045"
in line 607, Z again lowers to .063"
in line 686, Z again rises to 1"
in line 690, Z again rises to .045"
in line 819, Z lowers to .090"
in line 948, Z lowers to .125"
in line 1077, Z again rises to 1"
in line 1079, Z again lowers to .045"
in line 1208, Z again lowers to .090"
in line 1337, Z again lowers to .125"
in line 1466, Z again rises to 1"
in line 1468, Z again lowers to .045"
in line 1567, Z again lowers to .090"