I recently bought a '90 Yamaha XV535. I cleaned the carbs and was able to start it. I then decided to pull the tank and flush it out, replace the fuel filter etc. While the tank was out I took the opportunity to weld a little tab that holds one of the side covers back on with a little flux core welder. At the time of welding the battery was out and all the connectors around the fuel tank were disconnected. Now I've put it back together with a new battery and everything works - except spark!

I'm here kicking myself really hard for being so stupid - welding with the ignition module still connected. But then I did some reading and most stuff suggests that just disconnecting the battery is enough.

I'm going over it again today cleaning and reconnecting all the connectors but I'd welcome any input. Have I fried my ignition or is there a chance it's just a dirty connection?

Not related to welding on the frame, no current goes through the part in question. Either something got damaged moving stuff around or there’s a bad/disconnected part of the electrical system. Check a wiring diagram for things like kickstand switch, kill switch, etc. These can cut spark. Also check all your grounds and weatherproof connectors.

Thank you. I started that process yesterday then remembered the welding and got really disillusioned thinking I'd screwed up badly. I needed some encouragement to get back to it!

Oh, hell, bloody kickstand kill switches. One of the worst things ever - I get the idea, but every one I've seen has gotten packed with dirt and become problematic

Check a wiring diagram for things like kickstand switch, kill switch, etc.

Or neutral switch! I just remembered - the other thing that's not working is the neutral light. So, that's my first thing to investigate this morning. Strange that it will crank the engine, but not spark - but I'm hopeful.

Edit - no luck yet. Cleaned the crusty connector for the neutral light and that's now working but still no spark.

I really wanted you to be right, but I don't think you are. While checking all the connections, I couldn't separate the one that connects the stator to the loom. When I finally got it apart, it looked like
inside.

With that damage there, I'm expecting that I've not only fried my ignition, but my stator and regulator/rectifier as well.

That looks like exactly what happens when a connector has too much current passed through it, and it is not uncommon for motorcycles to suffer this kind of failure from loose/corroded connections. Unless you grounded your welder to one of those components instead of part of the frame near your weld, though, there’s no path for electricity through there from a welder. I still suspect you coincidentally found an existing problem, but fortunately all of those components can be fairly easily checked with a multimeter. Start eliminating possibilities with a wiring diagram for your bike, and a service manual, if you can find one.

That looks like it got heated and melted, electricity usually takes the path of least resistance, if that much current would pass through the wires you'd see the plastics around the wire melted as well, use a multimeter to test weather there's a wiring issue.
I also suggest check your battery

You could be right - that connector is the only one in that bundle that I had not previously disconnected so I can't rule it out as a preexisting condition. I'll keep looking.

Sometimes my starter switch gets stuck closed after the bike is turned off, and the battery will be too weak to start after an hour. When that happens, kick or push-starting saves me from having to jump it.

What voltage does your bike run on 12v? Your fux core welder you probably ran it at like 17-20v doubt that you hurt anything with that low a voltage.

I did a quick search and found this manual.
https://www.viragos.info/media/kunena/attachments/1518/1_pdfsam_manualdetalleryamahavirago.pdf

It’s usually pretty easy to find all sorts of service manuals, sometimes they’re scanned PDFs but better than nothing. I have one for my bike, my car, and my lawnmower lol

Try this link for a wiring diagram:

https://drive.google.com/drive/u/0/mobile/folders/13TttlH9fJnzFSQlDkB-GYDEXsNu7FPoe?usp=sharing

Thank you again. You were correct - I have not fried anything and it's now running again. I can't explain it - I gave up after finding this melted connection. Then came back to it, measured the resistance of the stator coils (which were all good) and cranked it again and it had spark! Maybe while measuring the stator I moved the connector for the pickup. Anyway - it's running and next time I'm in town I'm getting a can of contact cleaner to go over everything again.

That’s great! Hopefully it continues to behave for you - I rescued an ‘87 750 Virago many years ago, and it was a quirky bike to get tuned properly, but a neat little project.