Here's what my '78 looks like under that right cover. The single fuse is in the upper left, in a plastic holder (with room for a spare fuse) .....

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Here's a close-up of the fuse holder .....

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If you have a fuse box instead, it would be up under the seat, sitting on top of the battery. Here's the one in my Special .....


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If you go here, you can download an E model manual with the proper wiring diagram .....

https://thexscafedotcom.wordpress.com/2011/01/10/xs650-manuals/
I have mine on the right side, not on top of the battery.
 

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So, with just the main fuse present and if the signals are the only thing not working, I'd probably start checking for voltage in the headlight bucket on Dark Green or Dark Brown with the signal handlebar switch activated and work backward to the Brown/White striped wire that feeds the switch and on toward the Flasher, Self-Cancelling Unit, etc. to see where (if) power is getting lost
 
The fuse box with 4 circuits is on later Special models (supposed to be on late '78 Standard too), but yours has the single fuse under the right side cover. The diagram I posted is a colorized version of the same diagram that's in the '78 service manual.
 
You don't have a fuse "box" with multiple fuses, just that single main fuse. Like I said, I'm pretty sure that's how all Standards came. They didn't get a multiple fuse "box", only the Specials did. So, you were using the wrong diagram. JP posted that '77 one because it's close to what you've got, closer than a Special diagram, that's for sure. But there's no need for it because you can get an actual '78 Standard diagram in the link I provided. That '77 diagram isn't exactly the same as what you have. For instance, you don't have the #30 resistor it shows, and you won't have the #32 diode either. There may be other differences as well, I didn't look it over real close. But why confuse yourself? Use the actual '78 diagram.
 
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This from '78, etal Service Manual; Take your pick.......
 
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From the 78E supplement manual. ............I like the B&W diagram, i can make seveal copies for each circuit. Here i have drawn in the colour for the indicator circuit and the rear tailight on in park and the associated Ground wires Makes it easier to get the diagram into my head to continuity test each circuit. it also helps to find mistakes in any diagram. Most have something.

Here i the Indicator circuit + the taillight on when key is in park.

The 77D diagram has gauge lights and taillight on, when key is in park. The 78E diagram only has the taillight on when key is in park. @5twins maybe can confirm what his 78E does and if the 78E diagram park circuit is right.

78E Indicater  tailight 2 copyright.jpg
78E ignition Intrament light 077 077 -copyright.jpg
 
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From the 78E supplement manual. ............I like the B&W diagram, i can make seveal copies for each circuit. Here i have drawn in the colour for the indicator circuit and the rear tailight on in park and the associated Ground wires Makes it easier to get the diagram into my head to continuity test each circuit. it also helps to find mistakes in any diagram. Most have something.

Here i the Indicator circuit + the taillight on when key is in park.

The 77D diagram has gauge lights and taillight on, when key is in park. The 78E diagram only has the taillight on when key is in park. @5twins maybe can confirm what his 78E does and if the 78E diagram park circuit is right.

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You the man! Thank you ALL for your help with this!
 
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