First off on the alternator, did you replace the rubber isolators when you put it in?
http://cyclemax.com/inc/sdetail/gl1500_alternator_dampener_kit/158744/29165
Are you saying the noise was there when the dealer ran it without the alternator?
The box of rocks.... Does it only happen in 1st, N, 2nd, and 3rd, goes away in 4th and 5th gears? If so the 4th/5th gear shift fork may be worn. Goes away with revs up a little? This happens on a lot of pre 97 GL1500s, especially if there were floorboards attached with heel/toe shifter as many would ride with their foot on the shifter between shifts and that puts pressure on the forks in the transmission. Honda's fix was to put in a stronger fork and gears in the Valkyrie and 97-2000 GL1500. They warrantied some of these transmissions while the bikes were under warranty. I have a friend with a 92 that Honda replaced the transmission parts for that early on.(If it gets bad it starts popping out of 4th gear. Yes you can ride it for a long time just skipping 4th gear without problems to the transmission)
A test is to point the bike down hill in neutral and then uphill in neutral to see if the noise goes away.
http://cyclemax.com/inc/sdetail/gl1500_alternator_dampener_kit/158744/29165
Are you saying the noise was there when the dealer ran it without the alternator?
The box of rocks.... Does it only happen in 1st, N, 2nd, and 3rd, goes away in 4th and 5th gears? If so the 4th/5th gear shift fork may be worn. Goes away with revs up a little? This happens on a lot of pre 97 GL1500s, especially if there were floorboards attached with heel/toe shifter as many would ride with their foot on the shifter between shifts and that puts pressure on the forks in the transmission. Honda's fix was to put in a stronger fork and gears in the Valkyrie and 97-2000 GL1500. They warrantied some of these transmissions while the bikes were under warranty. I have a friend with a 92 that Honda replaced the transmission parts for that early on.(If it gets bad it starts popping out of 4th gear. Yes you can ride it for a long time just skipping 4th gear without problems to the transmission)
A test is to point the bike down hill in neutral and then uphill in neutral to see if the noise goes away.