Popping on deceleration means a pilot circuit air leak, or a non-working Automatic Coast Valve.
Both easy fixes.
The pipe is not the issue. The better pipe has leaned out the pilot circuit too much, and you need to compensate for it.
Usually, cleaning the ACV parts, a fresh fuel screw o-ring, and proper fuel screw adjustment is all you need.
Most people do not adjust the fuel screw correctly, and just make the problem worse.
My head is stage 3 ported with YZ cams, and a full race loud pipe, and I get ZERO deceleration popping.
I don't disagree with your diagnosis. There's no question that the thing is running too lean between zero and 25% throttle -- which (as you sat) points a finger at the ACV and/or the pilot circuit. The bike runs fine from 25% throttle and up. And I can control the popping by simply pulling the choke out. That tells a story as well.
I have pointed this out to the dealer (who has the best Yamaha service reputation in this area) and he tells me he's checked and adjusted those things when he rebuilt the carb. He blames a basic incompatibility between super low restriction race pipes and WRs at altitude.
I appreciate what you are saying and believe that your specific experience with this bike and this carb is important. But I'm not sure what else I can do, other than find another tech and go on a fishing expedition. Eddie Sisneros (Sisneros Speed Works) has done fine tuning on the FCR on my DRZ400 and it runs great -- but he's principally a Suzuki guy.
So, I'm gonna re-fit the heavier and more restrictive stock system and see if it cures the problem. I'm also expecting the bike to quiet down a lot with the factory pipe -- which is also important where we ride. Yes, I'm gonna add pounds and subtract horsepower, but I'm betting this bike will still feel pretty fast and light compared to my DR-Zs. I'm also adding a hand adjustable pilot screw (although the dealer has advised me it is "not needed"). I've worked on too many car and bike carbs over the year to believe that the idle/fuel screw is a "set it and forget it" kinda deal. We ride from 7k to 12.5 k feet above sea level -- and you've got to be able to quickly compensate for 5000 foot changes in elevation.
If going back to the stock setup doesn't fix the problem -- or creates new problems -- the bike will go back to the dealer as a "Come Back."
Again -- I appreciate all the advice you and others here have given me, but I have to give the dealer a chance to prove or disprove his theory that the FMF is the problem -- not the carb.
The good news: Riding season here won't really start until March/April. And then it will be in the western desert -- not up here in the clouds. So the dealer and I have a few weeks of experimentation before it cuts into my riding time.
Thanks again for the all the advice!