All good advice.

The free-spinning resistance should be near zero, no noticable difference from the original 65a. The difference in resistance comes from putting a load on it.

Since the alternator won't be putting out any more net watt-hours, it won't affect power nor mileage. In a nutshell, the original alternator needed to rely on the battery to fill in the extra power output at times, and charge it back up when there is surplus power available. The new alternator will be able to simply keep up with the loads in "real time". Even additional rotating mass (if there is, it's a more efficient design) won't show on a dyno, as it's minor compared to everything else, and a dyno is typically looking at stabilized output, not how fast the engine can free-rev.

Your direct cable should go to directly to a load, which should be the fusebox. The battery should be connected to the fusebox also, and directly to the starter, this is the most efficient.

As far as cable, you don't have your location listed, but if you have a marina nearby, the best cable IMO is boat cable. This is thin-stranded like welding wire (which would be my second choice) and very flexible, pre-tinned, and the marina will likely have a crimper for proper cable ends.