Different voltage at trunk vs alternator suggests 1.1 to 1.3V drop in voltage, about 5 to 10x more than desired. That indicates poor connections, terminals, or too small of cable.(s). That would also make cranking engine difficult. We do not know how the wiring was done.
67Dart273 suggested an AC measurement, what reading for that, at alternator stud?
The battery is the filter for the alternator ripple, having it electrically remote, increases voltage ripple. The less ripple when fans are on, suggests the back EMF from them is helping, so do test with them off.
