Use the Mach3 Parameters -
#5221 is G54X, #5222 is G54Y, #5223 is G54Z, #5241 is G55X, #5261 is G56X, #5281 is G57X and I think you can see the pattern here.

#5241=[#5221 +.875] (or whatever the distance is)
#5242=#5222 (so the Y is correct)
#5343=#5223 (unless the Z locations change)

And repeat for each tool.
You can put this in its own .NC file or at the head of each file that uses that tool block

Also works for general milling -
Set first tool
G54
M98P1
G55
M98p1
G56
M98P1
Set Second tool
G54
M98P2
G55
M98P2
G56
M98P2
and so on