'79 XS400 only running on one cylinder

Miles

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Hey everyone! New to the forum, but been around small engines most of my life. I just recently picked up a '79 XS400, and decided to get it running again (present for gf for getting into Vet School). I got it running, but only on the left cylinder, and I'm stumped as to why. Here's a list of everything I did to it to get it running in the first place:
-changed oil/filter
-cleaned gas tank from rust/varnish deposits with vinegar and BB's
-thoroughly cleaned carbs with carb cleaner and compressed air
-changed fuse box with updated unit that used blade style fuses (old buss fuse holder were corroded and causing bad connections)

Got the bike to fire and I thought everything was good, but it wouldn't rev up when I applied throttle. It idled fine, but as soon as you applied throttle it bogs and dies. Pulled the cap off the right side while it was running and realized it wasn't running in the right cylinder. Pulled the plug, laid it against the head, and noticed that I DO have spark. The spark plug was also wet with gas, so I know I'm getting fuel to the right side cylinder. I'm currently stumped as to why it's not actually running on the right side. What should I check next/swap around to see if we can find the root of the cause?

Any help would be greatly appreciated. Also, here's a picture of the bike.

Thanks!
 

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Nice sled. Checked compression? Fire with just a drop off starter fluid in it?

If so, probably carbs not fully clean, not bench synched, not synched on bike, or incorrect float height. Did you do all those steps? What's your float height?
 
Nice sled. Checked compression? Fire with just a drop off starter fluid in it?

If so, probably carbs not fully clean, not bench synched, not synched on bike, or incorrect float height. Did you do all those steps? What's your float height?

Haven't checked compression in that cylinder, but when turning over the engine by hand it feels good (read feels the same as when the left side is under compression). I'll clean the carbs again, but if I'm getting fuel to the cylinder, why would you think it's a fuel issue? And floats are set same as they were from the factory.
 
Timing, compression, points clean and gap, carb sync with manometer, valve adjustment. Fully disassemble and clean carbs make sure the idle/pilot mix screws are not broken off in the carb bodies. This is very common with your year carbs. Start with new plugs and caps. Your bike has aftermarket mufflers on it make sure someone has not put too big of jets in the bike. Start with stock sizes first. Most specs and info you need will be in the manual which is in the forum.
 
Timing, compression, points clean and gap, carb sync with manometer, valve adjustment. Fully disassemble and clean carbs make sure the idle/pilot mix screws are not broken off in the carb bodies. This is very common with your year carbs. Start with new plugs and caps. Your bike has aftermarket mufflers on it make sure someone has not put too big of jets in the bike. Start with stock sizes first. Most specs and info you need will be in the manual which is in the forum.

Forgot to mention it has new spark plugs. And I'm pretty sure those are factory mufflers. If they're aftermarket, can you link to what exactly they are?

Carbs have been completely gone through and cleaned, nothing is broken or missing. The cylinder is getting fuel, like I said in my original post...

Also something pretty important as to why I truly don't think anything is out of adjustment... The bike only has 5k miles on it. If everything like float height, valve adjustment, timing, etc gets messed up in that few of miles, Yamaha wouldn't still be selling bikes.
 
40 years of sitting on parts can cause oxidation and drying out. Don't care how many miles on it. If it was stored dry and clean in a perfect climate controlled area maybe, but it would have been very well taken care of. Those are aftermarket mufflers. They look like MAC brand but hard to say. If your plugs are wet than your getting too much fuel. A wet and dry compression test would be a good start.
DSC03663.JPG Stock 78-79 xs400 mufflers.
 
Make sure the pilot mix screws are long and pointed and the hole in the carbs are small like the tip. These break off easy and people drill them out with large bits which destroys the carbs.
DSC03664.JPG
 
Squirted some starter fluid into the right side carb, and still not getting it to fire (also still getting spark). Now what?
 
Finally got it running smoothly. Spark plug on right side wasn't gapped correctly, and even once gapped, wouldn't work correctly. Trip to the parts store to get a new spark plug, and took the carb apart and cleaned it again, and it finally started running right. After a few trips up and down the road, everything finally broke free, and it's running like a top.
 
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