A couple things I've been thru on this topic.
My Valk sat for a bit, (several months) while building the hack rig. Every few weeks I would start it and bring to temp, and it slowly just started running like crap. First number 5, then #3 pipes were slow to warm up, then stayed cold. F'ing ethanol. Time to rebuild the carbs.
When you emptied your tank, did you TRULY empty it? When I rebuilt my carbs a couple weeks ago, I emptied the tank by removing the filler cap, and holdingshaking/turning while it was upside down. There was still a little fuel in it, but (at the time) I did not know how bad it was. Later when I emptied the fuel from a oil drain pan into 1 gallon jugs for disposal, it was incredible how much milky white cr@p was in there.
SH!T. Pulled the tank back off the bike, and this time I inverted it, and removed the petcock for draining.

Pulled another about 3 oz of white milky stuff. This time I then let the tank air dry, then rinsed with clean (new) gasoline. If you did not do this last step, you may have just re-contaminated your system.
Re: testing for spark. Be very cautious that your running rough is not being caused from a stuck float by crap in the fuel. On the GL1200 and the Valk, the vent just spills onto the top of the engine cases; allowing stuck float to pool fuel there in casing depressions. Dealing with a rough running GL1200 a few years ago (later traced to EMGO filter glue breaking down due to ethanol eating it), I pulled the plug, put the cap on, and hit the starter with the electrode grounded to the engine case.
I was rewarded with a spark. And then ignition. OF THE POOL OF GAS ON THE CASES. Not a big fire, but big enough to get my attention.

Grabbed a rag to snuff it out. Which happened to be the rag I had used to clean up with after changing the oil; and then cleaning the oil pan with gasoline. The rag ignited a lot faster than I had planned.
Pulled the rag out from the cases and tried to snuff it out on my levis. Another bad idea, after working all weekend and wiping oily hands on my pants. Lit my frickin pants on fire! Again, not a big fire, but it got my attention.

Now I have 3 things on fire within about 10 seconds. I'm thinking DAM, this is like an episode on that quirky show a few years ago called Dead Like Me. When your number is up, Gravelings show up and make things happen to ensure you get to your destination...
But I got a mulligan; a handful of sand on the pants, throw the rag down the driveway (away from the car and the weeds), and a few more handfuls of sand on the cases put the fire out. In case anyone needs to know, that cool paint that is sold for carbs burns very nicely. But I digress...
Funniest part is that when the last fire was out, wifey stuck her head out the door. "Are you ok? I heard yelling." There is an acrid smell of burnt wiring and hose in the air; thankfully, no skin. "Did you have a fire?" Well, just a little one; everything's ok. Could you get me a beer?
Be careful testing for spark. And I'd suggest a fire extinguisher in the garage...