Perhaps I am misunderstanding or not seeing something, but my understanding is MagicLauncher injects the files (which is what I'm assuming you're referring to as "Magic launcher [letting] me do this directly".). As such, the below photo shows exactly that - Magic Launcher is set up to inject the majority of the mods except for some NEI modules that were finnicky. Maybe I'm missing some "Install these files directly to minecraft.jar" button, but I believe I'm set up correctly as literally everything else works except when I try and load this mod.
Ack.. Badwrongno. IC2, Railcraft and others set to be in the jar? *WRONG* way to go about doing things there.
the *only* things that go in the jar are:
Forge
CodeChickenCore
NEI
Optifine.
everything else goes in the mods folder.