buddha,
Were you able to get someone to tell you what was wrong with the old alternator? Taking the fuses out sure wouldn't hurt. You can test the alternator on the truck by temporarily touching a jumper from the battery, or a battery source to the "F" (1) terminal on the regulator. You need a meter on the system when you do this. This test will energize the alternator field and make it charge its max. If you do this, and the alternator is good, the meter should jump to 14 + volts.
If some wiring glitch toasted the previous alternator, you don't want a repeat performance. I don't really understand what you meant about the battery post grounded to the fender. You don't want to pull cables when the truck is running.
A internally regulated alternator would have been a better choice from a simplicity standpoint. Study the directions that came with the harness. Verify all your regulator connections. #2 terminal should be switched with the key..key off, no juice.
Jumping 12 volts to the field terminal will tell you if the alternator works.
Removing the fuses can't hurt
Internally regulated gets rid of the troublesome regulator.
Sit down with a cup of coffee and study those instructions for the harness. The horn wire and taillight issues are minor. It is starts, which it does, and if it charges, which it WILL, the other things on the list will soon be solved.
Stuart