Can you picture the battery cable? You may be confusing the wire which goes from the starter relay "square" screw down to the starter solenoid. This would be a separate wire with an eyelet on each end, but may be molded / wrapped with the main cable. ORIGINAL type cables had the starter end molded together, so the main bolted to the big stud, and the solenoid wire bolted to the solenoid.
Since you are upgrading wiring, it makes NO sense to run no10 from the alternator, most especially if you have gone to a larger alt. Use at least no 8, or another way around it is to use two or three no 10 in parallel
The red and black at the starter relay are both HOT not switched with the key. If I understand "what you did" the red and black are the old ammeter wires? You now have them in parallel, which means these two wires are doing one job......feeding power into the interior of the car
Now matter how you do so, the battery, starter, starter relay, alternator, and the power feed (red and black) into the interior must be all tied together The thing is there are different ways to rout this
Post a photo of the unknown wire in your new harness. It sounds like voltage regulator hookup
PLEASE POST THE YEAR MAKE AND MODEL