Well I think I have resolved (mostly) the backfiring problems on the wifey's S40. I learned a lot reading through the posts here. I'm gonna provide a brief summary of the steps I went through in case it provides any help to others. Everything I did was referenced on other posts to some degree.
It all started with the nasty backfire. It was ALL the time.
The first thing I did was the white spacer mod. Replaced the stock spacer with a #4 nylon spacer that I got at the hardware store. I had some trouble trying to get the carb out. So after reading here I decided to spend a couple minutes to remove the battery box (4 bolts inside). Should have done that right away as it gave so much room to take the carb out. I was fortunate in that all the carb screws came out easy. As recommended, I replaced them all (4 on top and 4 on bottom) with hex cap screws.
When backfiring continued, I noticed a HUGE exhaust leak where the stock muffler attaches to the header. Instead of trying to fix that I thought it would be a good time to replace the muffler with a stock Dyna muffler.
I removed the full exhaust in order to have more room to fit the Dyna muffler. The opening of the Dyna muffler was a bit loose to fit the head pipe, so I cut up some aluminum cans and used some High Temp RTV sealant. The dyna mounting points fit on the S40 support bar. I used two carriage bolts and was done.
I fired up the bike, and the backfiring was still bad. Time to rejet.
I bought a Stage 1 kit from DynoJet (if I could go back I would have taken people's recommendations and gone with Lancer's kit as the DynoJet costs more and does not include a larger Pilot Jet). I put in the jet DynoJet recommended. It was easy to do with the new hex screws. Took all of 5 minutes.
Backfiring was still there...but it was different. It was now firing on accel instead of just decel. However even with the backfiring, the engine ran nicer and I could feel more power when I took it for a spin.
So...after further investigation I found that it was leaking at the head (where head pipe meets cylinder). I tried tightening it and it helped..but just a bit. I read that loosening and then re-seating it might help (I should mention I put in a new exhaust gasket as well). I removed the full exhaust and this time tried to make sure that the head pipe gets seated and secured better first. When I did that I realized that when you put on the Dyna muffler the line of the exhaust is not true to stock. I had used two carriage bolts to secure the Dyna muffler and that forced the exhaust to be mis-aligned. To make it a better fit, I just used the front bolt on the muffler. That helped.
I tightened everything up...and no backfire. Woohoo. We took it on a 40 mile test run..highway and city to see how it held up. the additional power was very noticeable. We had 1 or possibly 2 backfires...but they both occurred on hard deceleration / downshift from 65mph to 0. We can live with that.
As the alignment of the exhaust is still possibly out a tad, there could be a small exhaust leak. We may look at going with the bigger pilot...but we need to run more to see how it goes.
We put the stock heat shield back on but could only use one clamp as the other is affixed to the stock exhaust. It looks like it holds pretty tight. When I went to put the heat shield by the footpeg back on I saw that it was pretty tight. To fix that I put in a couple washer/spacers in there to lift it away from the exhaust enough.
So that is my story
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