Maybe to keep everything more managaeable and readable, you should translate theoriginal script into Python - that way you willhaveno surprises on otherwiser trivial things as variable assignment, picking elements from sequences and so on.
1 and 2) your calls are apparantly correct to flaten an "add an alpha channel " (not "alpha layer",a s you write, please) to the image - but you are calling color-to-alpha to make White (255 255 255) transparemt not black. Trey changing that to (0 0 0) - if it does not work, make] each of the calls individually, either on script-fu console or on python console, and check what is wrong.
3) Script-fu can't return values to the caller (as can be seen by not having a "return value type" parameter to the register call. That means that scripts in scheme in GIMP can only render thigns on themselves and not be used to compose more complex chains.
That leaves you with 2 options: port the original script to Python-fu (and them just register it to return a PF-IMAGE) - or hack around the call like this, in Python: create a set with all images opened, call your script-fu, check which of your images currently open is not on the set of images previously opened - that will be your new image:
The tricky part with this is that: there is no unique identifier to an image when you see it from Python-fu - so you 'dhave to compose a value like (name, number_of_layers, size) to go on those comparison sets and even that might not suffice - or youg could juggle with "parasites" (arbitrary data that can be attached to an image). As you can see, having the original script-fu rewriten in Python, since all the work is done by PDB calls, and these translate 1:1, is preferable.