Alright, first of all, thanks for taking a look at this little problem!
Since I got it a month ago it has never fired for me on the right cylinder. I have the parts manual and a service manual from another xs400 of the same year so feel free to reference them. I'm putting the bike back together and here's what I've done to try and fix or diagnose:
-Took the carb apart and cleaned it, checked the pilot screws and one was all the way in so I backed it out 2 1/2 turns as per the service manual.
-Put in brand new spark plugs, caps, and spark wires on both sides. I have checked and there is spark on the both sides.
-Checked what was coming out of the exhaust of that cylinder and it's gassy air.
-After a few minutes of reluctant idling the left exhaust is hot hot hot, and the right is not not not.
So there's at least some gas - I don't know if it's the right amount - and there's some spark, but it feels like it's not firing at all. I have a worse condition carb I can swap in that was sold as "working good." I'm about to try that.
Thanks again for looking and for sharing any thoughts.
Aaron