I think what you want to do is build each step into a function. These functions can be stored in the same script file or in their own module that gets loaded with the import statement (just like arcpy). The pseudo code would be something like this:
#file 1: steps.py
def step1(input_files):
# step 1 code goes here
print 'step 1 complete'
return
def step2(input_files):
# step 2 code goes here
print 'step 2 complete'
return output # optionally return a derivative here
#...and so on
Then in a second file in the same directory, you can import and call the functions passing the rasters as your inputs.
#file 2: analyze.py
import steps
files_to_process = ["raster1.tif", "raster2.tif", "raster3.tif"]
steps.step1(files_to_process)
#steps.step2(files_to_process) # uncomment this when you're ready for step 2
Now you can selectively call different steps of your code and it only requires commenting/excluding one line instead of a whle chunk of code. Hopefully I understood your question correctly.