on your 2003 you need to carefully check the following regarding possible causes/cures for your situation:
1-check to see if your factory sidestand switch is still installed. look at the stand by the mount. see the little button switch? remove the 2 wires.....source a quality MULTI-METER....place it on ohms...kickstand down of course.....pin the multi-meter leads to the 2 pins on the switch....read meter and work the button in and out on the switch. see dramatic change in meter readings? if so switch is ok. if not switch is faulty. replace it.
2-a stator or VR on the way to death-row will typically activate your CEL telling you a charging system fault OR low voltage issue has occurred. check that both cable ends are perfectly clean and secure to the battery.
3-wrong fuse placement? you must be referring to the diode fuse. when installed correctly the arrows point to the drive belt side of your XB. if wrong turn it around.
4-replace your battery fuse. it's 10 cents.
5-remove black plastic front pulley cover. see the large bundle of wires coming in from motor side that attach to harness plug then head towards battery area? that is your 77 connector. unplug....check for arcing/corrosion/burned connector spades....spray with kano kroil...reattach.
6-perform simplest charging system test known to mankind. others will chime in with lofty schematics, beautifully colored diagrams, incredibly complex instructions and other assorted jibberish. it's all bull****. take your multi-meter and set to DC VOLTS. start bike...warm motor...hold throttle @ constant 2500rpm. should see 13.2-14.4 volts.....in that vicinity is fine. do you?
the above check-list will get you started. you might have other issues but what you described is electrical interruption in nature and typically sourced to either the battery or charging system. report back with findings please or i get grumpy.