so you need a multi meter to run some tests. hopefully you have one, if not they should be under 10 bucks at most places.

So lets run through how this works to make sure we all understand what happened.

you had a 100 amp alt. Based on the year of the truck, it should be a dual field alt.
you replaced it with a 60 amp you had laying around.
Again, please let us know if it was a dual field alt as well? Just making sure.

This suddenly stopped charging as far as you know.

There are 3 wires to a dual field alt.
2 field wires and then the big post out of the back of the alt.

1 field wire goes back to the VR. This should be some value less than 12 volts with the key on.
1 field wire is battery voltage with key on.

the big alt wire you have said you wired directly to the starter relay, on the big stud there, which also has a wire directly back to the battery.

This should also read battery voltage, with or without the key on.

The original wire that used to go here, you have removed.
you still have power to the inside of the cab which means you still have power going in.
This is really independent of the charging system, other than the key on parts.