Bit of a stumper, so I'll see what the experts have to say.
Went for a problem free 70mi a ride a few days ago on the 400. I pulled into a gas station for a fill up and as I was turning in, the bike backfired.
Filled up with gas and then the bike started up running on one cylinder. Checked for spark and found no spark on the right side. Swapped plugs still no spark on the right side. Left side was fine. Pulled the tank and swapped the lead wires going into the coils (NOT the plug wires.) Right side now had spark, left side did not. This lead me to believe the problem is not the coil and is further back possibly the ignition module.
Put it all together. Started the bike again. Idled only on the left. I noticed I was getting spark on both sides when the revs were up. I made it the last 14 miles home but spark on the right side was not consistent. The next day, both sides were sparking fine when kicking it over. I have not ridden it yet to see if it the right side kills again, but I assume it eventually will because I haven't changed anything.
Details:
Dyna S ignition, new HVC wiring harness, OEM coils with ballast resistor. Spooner and I secured the junction between the stator and wiring harness and also checked timing last weeked to work out some other issues.
Any ideas?
Dyna usually work or don't work, but sometimes they breakdown when hot. I'd try another module. buy the cheapest working DYNA S you can find and strip out the modules.
My dyna did that then other day. My right coil likes to fire twice instead just once. Something is up with the module.
Organicjedi, you have described my situation with my RD400 almost exactly. I have Dyna S pickups. Bike goes like a missile until it mysteriously will stop sparking on one cylinder. I had a set of the Economy coils on it, so I went back to stock. Ran great, then suddenly after many miles, it is back to a one cylinder RD. Limp home. Sucks. Wait awhile, wind changes direction, and suddenly it is a missile again. I have eliminated the coils, 7mm wires and spark plug boots. Only thing left is the Dyna S pickups.
Will look for set from ebay or wrecking yard to start swapping them out. Will update when I solve the problem.
I recently had some misfires and thought it was jetting but found out that my bikes timing slipped but ran fine when it was cold and etc. Retimed and it was fine. I am currently running fake dyna modules with vintage smoke rotor and bracket. My old modules went to shit...someone left the key on and it fried it. Don't use your kills witch, use your key!!!
Aside from the potential Dyna issues, honestly check the torque of your heads. If they crack loose, you'll get backfires from air being pulled into the cylinder through the head.
This is a fascinating problem; I'm sorry you're struggling with it, but curious to learn what the cause is. You'll find it!