As to your original questions.....
"If I run the hot wire back to the fuse box at the "ignition" connector, will I need to install a fuse between the on/off switch and the fuse box?"
That would depend on if the "Ing" connector you are tapping into is protected by a fuse and which side of the connector you tap into. If you tap into the always hot side of the connector then yes you should put in a fuse and it should be at the same rating as the max amp draw of your fan....... If you tap into the fused side of the connector then .... no you don't need a fuse, be warned, if your Ing connector fuse is smaller than the max draw of your fan .... you will be replacing some fuses and I would not recommend you put in a larger fuse to compensate because then you byspass the lower amp protection to the original circuit it was protecting etc....
"Or will the ignition connection provide the required protection?"
"Can I ground anywhere, or should I ground at the on-off switch?"
There are two ways to do this..... ground one side of the fan and run a pwr wire back to the Ing connector, as you mentioned above..... or Run the pwr wire from the Ing connector, as you mentioned above, to one side of the fan..... making the fan Hot at all times then running the other leg from the fan back to one side of your switch and the other side of the switch to ground.
You have to make up your mind how you want to wire it...... both ways will work....... But I still recommend you use a 3 dollar relay and wire as explained in my eariler post.