Mornin' Gene...you may confuse folks when you say "The starter relay is getting power as well as the starter motor."
thats probably if you jump the big lugs on the starter relay, correct? if so, starter relay is connected directly to battery...thats why its hot.
If not so, quit reading reading here. otherwise...
...your main power switch (keyswitch) has probably failed, common problem on your year/model bike, ...red wire supplies 12v from main fuse into switch. Brown wire supplies power out..guessing no primary power out on brown wire...for lights, cdi etc etc..confirm with DMM, test lite etc
after you replace the switch and fix the bike, remove the 2 plastic clips and pull the back off the old switch, ..you'll see the failure point..small springs load the switch wiper arm against the contact pads, those springs rust and break thus no contact..not bad service for 16 years...
oh bite the bullet and get the yamaha oem switch..the supercheap ones you find on ebay are often intermittent.
walt