I've got an '08 AE. If you can, it may help future posts to have your year/model in your signature.
For maintenance, replacing the clutch fluid (if it hasn't been done) should be looked at. Mine had not been serviced by the previous owner and it was past due. The new fluid made a noticeable difference.
There is some "getting used to it" when you move from manual to auto-clutch. Coming to a stop there can be a slight "push" in 1st gear until the clutch engages. I got into the habit of rolling up to a stop in 2nd gear. You will feel the bike apply the clutch and shifting down to 1st at that stage will not lock it back up unless you apply the throttle. For me, it disengages from 2nd at a much better rpm band.
Some members have changed the programming to engage/disengage the clutch at higher rpm's in 1st to address the "push issue". I actually like the lower rpm clutch activation in 1st gear. I use slow speed maneuvering enough to need lower rpm power in first, especially in 2 lane U-turns. I have found if I'm in 1st and feel that "push" starting to happen when I'm coming to a full stop, I can take a quick stab on the brakes and the clutch will engage and I can roll forward on inertia alone from that point.
Another somewhat unique experience is a shudder that can happen before it is warmed up. I found that allowing the engine to warm up to the point that it comes off the high idle reduces it tremendously if you are experiencing this. I very rarely experience any shudder after warm up.
Some members resort to soaking their clutch plates trying to help a shudder. It isn't an overly difficult procedure although you need to be specific about reinstalling in the same orientation as removed. Most have found dryness, but after a lot of reading and watching the results, or maybe the lack of positive results, that most experience, I have accepted that this is a quirk of the auto-clutch. Albeit, a very manageable one.
Use a JASO MA or JASO MA2 rated motor oil. If it has the rating it will be listed on the back. I DO NOT want to start an oil thread, but it is a wet-clutch and staying with the rating will eliminate one possible issue (if you are having one).
Lastly, there is some jerkiness in low rpm maneuvers in 1st gear. You can drag your rear brake a little and it will minimize the jumpiness as you apply throttle. Practicing low speed U-turns in a parking lot helped me immensely.
There is an adjustment for the free-play of the throttle and it is worth your time to minimize the "dead-zone". The adjuster is just down the cable from the throttle and is covered in black plastic that you will slide up the cable, which will expose the adjuster and lock nut. Super easy.
Many members have had their ECU's reflashed with new programming from Ivan. According to those that have done it, Ivan has substantially improved the drivability and has specifically addressed the low rpm jerkiness. So, there's an option for you there as well.
The most embarrassing moments are my fault.... when I forget to turn on the auto-clutch after filling up or something. I'll start it in 1st (kick stand has to be up) and pull away feverishly flicking the paddle hoping 2nd gear will engage... only to look down and not see a green light...
Really hurts the "I'm cool" factor...
"The only barrier to knowledge is the belief that you have it."
2008 Yamaha FJR1300AE
2002 Honda ST1100