Update:
So I haven't found an "A" model MCU yet, but I was making some adjustments to my "AE" and solved some of my complaints with the "AE".
1) My biggest complaint is the "AE" initial clutch engagement. It is typically clunky and aggravating, especially at low speeds... there are times that it doesn't seem like it knows what it wants to do, but most "AE" owners already know that.
2) The upshifts tend to feel lazy, not snappy like you can get with quick shifts of a manual. The downshifts also seem to be lazy and does not drop a gear quickly... there is a moment of clutch slippage. This would be the same as downshifting a manual and releasing the clutch very slowly. It is very difficult to downshift and match revs when the "AE" is being lazy.
The answer:
While in YCCS diagnostics on the digital display, you can adjust "SH66" to raise or lower clutch engagement RPMS. I have monkeyed around with this on more than several occasions and finally figured out the best setting. While in "SH66" mode, lower the RPM engagement all the way down until the green indicator light won't blink anymore. This allows for the lowest possible initial clutch engagement, which is approximately 1150 RPMS. Not only does this give you off idle throttle input, but I found that it also controls the clutch spring engagement rate. In other words, upshifts and downshifts occur the instant you shift and feels very firm without the laziness.
The other solution is adjusting the CO settings, which has been talked about numerous times on this forum. I orginally increased my CO settings +7 like most on the forums reported. But after making my above "SH66" adjustment, I still had off idle throttle stumble. I then increased the CO +2 for a total increase of +9 and it has absolutely cured my off idle stumble. It should be noted that my FJR is completely stock and my location is 584' above sea level.
Summary:
After making the above two adjustments, I feel that the "AE" is substantially better than delivered by Yamaha. The rideability is vastly improved and very predictable, which most "AE" owners complain the most about. I still don't have the full control that a manual would give me, but I am very happy with the results...
My next endeavour will be fabbing a shift linkage to replace the stock linkage in an effort to eliminate the clunk of the "AE" shift actuator... think dampeners inline with the linkage. Although the stock linkage already has that, it just sucks and doesn't work.
Take care,
Dan