I spent twenty minutes looking for a picture of it but Ford finally added the bypass kit in 98 or 99 and a major part of it is a braided ground wire that goes from the water pump to the heater core.
Also the Impeller on the Vulcan waterpump is notorious
If you run a bottle of Prestone Super Radiator Cleaner it will help.
I had the Brown Coolant problem on my 99 Vulcan.
I flushed my system until it was nice and clean only to have it come back.
My 99 had the Bypass hose kit installed but did not have the ground that goes from the heater core to the water pump.
EDIT: didn't realize I posted in the 2 year old link. Sorry
This is how I finally made it go away and it hasn't returned.
1.Totally flush the system with the Prestone Radiator Super Cleaner.
2.Pull the Heater hoses and flush and flush and then back flush and back flush
Flush and flush and flush then
Back flush ,backflush,backflush
Hook the hoses back up and run it for a while with straight water
3.Change the water pump
4.Run another bottle of Super Radiator flush for the proscribed 6 hours.
5. drain and pull the heater hoses and flush and flush and well you get the picture.
6. make sure you install the ground wire. I grabbed one from the salvage but you can just make one.
7. Change the Expansion tank/resovoir with the current updated version.
8. Fill with the proper amount of anti freeze.
It's been 4 winters and now brown coolant or no heat problems.