Dyno tuned/ CBR1000RR - mid range loss

Two years ago I installed the Bazzaz Z-bomb on my ’09 CBR1000RR which restored the original top end performance. The new power was felt immediately in the top end. The next year I replaced my stock exhaust with a Yoshimura R-77 Stainless/Titanium Full System, added the Bazzaz Z-Fi fuel control unit and brought the bike in to be dyno-tuned for custom mapping. After the dyno tune however, it felt like I lost some power in mid range. HP overall was increase substantially, but that mid-range pull - which was really what made riding that bike so enjoyable- seems to have been decreased. Did the dyno tuner mess up somehow? Why have I lost that mid-range?
 
I also purchased a Z-AFM custom fuel mapping unit as well, but I still need to modify the exhaust to allow for the installation of the sensor. I am hoping this will help. Before I do that, I would like to know what happened. Any ideas?  

Unless the dyno is an "eddy current" unit (or a brake dyno), it's a hit-or-miss operation to actually tune it correctly. The reason is because the more common inertial dynos only really measure full throttle power, due to the load which can't be maintained for long enough periods at lesser throttle position/rpm settings to make any sort of real tuning decision. Also, it's a common mistake for a lot of shops equipped with a dyno to shoot for high peak readings at the expense of numbers "below the curve" because a lot of customers only care about peak readings.

There's also the possibility that the increase in top-end power has suddenly made the midrange "feel" weak. But it sounds like you've ridden your bike long enough to know the difference. Do you have any dyno charts from your bike when it was stock?  

No, unfortunately I pulled the stock exhaust  before I went to get it tuned,
and they didn't run it on the dyno before they installed the Bazzaz z-fi. They did provide me with the map though. I don't know if the the dyno was an "Eddy Current" either.
I was thinking the Bazzaz autotune self mapping module might correct this.  Any thoughts?  

In theory an autotune self-mapping setup would get your engine running at its best, but a lot can go wrong between here and there. We've had instances where the autotune (admittedly not a Bazzazz module) suddenly decided to stop working, and the only reason we knew is because of a slight hiccup at partial throttle. Still, YMMV, and we know a few who swear by it.  

I'm thinking of using the autotune sparingly and only to create a new map and bring the midrange power back, and then possibly even removing the sensor afterward and plugging the exhaust. If I use the auto tune,  do you think it would bring the midrange back?  Would the autotune recognize that the midrange needs to be punched up, and if so, does this mean that the map I had created with the dyno was done incorrectly? I'm just trying to get me head around this whole issue. I'm getting the feeling that the whole dyno tuning business is a bit questionable. What if I just removed the bazzaz Z-fi. Would running the stock fuel map hurt the engine with the yoshi full exhaust?

Any further advice is appreciated.  

The autotune is not guaranteed to bring your CBR's missing midrange back; it cannot "recognize that the midrange needs to be punched up". It will only bring the A/F ratios into line with what it sees as the optimum for that rpm/throttle position. Whether that results in filling in the midrange is the big question.

As long as any "dyno tuning" is done with an eddy-current or other type of dynamometer that puts a constant load on the engine at specified rpm (not just spinning up a weighted drum), then it can result in optimum performance.

It probably wouldn't be a good idea to run your CBR with full exhaust without some sort of fueling modification, because the increased flow will most likely result in lean A/F ratios at numerous spots in the rpm range. The stock O2 sensors are only made to modify idle and very small throttle opening fuel mixtures.