You can patch a main.dol file with your gecko codes inside of a GCT (Gecko Code Table) file using WSZST. You'll then have to modify the pack's XML file to include the main.dol folder. For example, I have a folder called "Codes" in my Pulsar pack so you can choose from several different modes.
Also, I'm not sure what your goal with point 3 is.
Also, I'm not sure what your goal with point 3 is.