Your best bet is to contact V/H as ask them what to start with as a base map for autotuning. I believe the monster rounds was what somebody here posted when they contacted V/H about CFR's....
The sled will run rough at first... yes... that is normal for the auto-tune process. As the learning process progresses, V/H recommends 'APPLYing' the populated table every so often.. like and hour of cruising.. check your table and APPLY. Then change your riding to stop and go city for an hour... and APPLY. What this does ( according to V/H ) is it applies the learned values to the base map and continues to learn.... this is like the fine-tuning process. The only downside is that the table returns to a blank canvas each time to APPLY the tune. IF you wait for a few hundred miles, you can check your table often and see what blocks have been learned and what has not. If you want to force an area that is not learned, you can use the TPS% and RPM of the unlearned area to make it learn. So if you have a high RPM range and High TPS% that you want learned... you can monitor the RPM and TPS% to force it to learn.. you may have to hit this range a few times to make it learn because it takes a few times in that area for the FP3 to populate that block with good data and not just a single shot.
After you apply a tune that has about 30-40% ... the bike will run smoother since you applied the learned values.
Once you are happy with the tune... you FINISH it instead of applying it. Then all the learned values are saved as your primary map.