Ok, the described way seems good in order to obtain the desired result.
You can get rid of the M104 commands inserted by Simplify3D by using the {STRIP "M104"} command in the Post Processing box, followed by a {REPLACE "New_M104" "M104"} command to transform your custom M104 commands written in your script (Start, Tool change, End, etc.) in correct M104 commands.
(Please note: "New_M104" is a custom name used for example purposes, you can use the string that you want.)
Anyway, in order to obtain a complete viable way, it's important to resolve this sort of "bug":
viewtopic.php?f=9&t=12972
Thank you!