Would I run a wire directly from the positive battery terminal to the yellow sled wire
Yes, but you MUST ABSOLUTELY use a weatherproof fuse block as close to the battery as possible. This is to protect your car from burning to the groud as a result of a shorted cable.
and if so where would i run the orange ignition-switch wire? Someplace to the fuse box??
Yes, to one of the the ignition-switched fuse points. However, if you're in this business to try and remove a ground loop, the ignition wire connection is much less critical and might not make a difference. On my installation, the yellow power wire runs directly to the battery, but the ignition wire is still connected to the factory harness. But if you're trying to re-do everything just to be sure, then yes, that's where you do it.
Above all, if you're going to be bypassing the factory wiring, the most important thing is to choose the most solid ground point possible. The correct location for the ground point is described
here.