I am seeking some understanding of how the AT work and if it does why is it no recommended by some. Here are a few questions:
1. Now that the bike was dynoed, would the autotune improve on what was done on the dyno?
Not necessarily. When you call for a specific A/F ratio number, it may not be what was "programmed" before. If the bike ran good before, the dynamic will change as with the AT "On" it will change the programmers values to match what is on the A/F chart.
2. Would it give me better fuel economy with normal everyday riding and more power when riding aggressively?
Again, not necessarily. It all depends on the values on the A/F table.
3. Does the autotune require me to make the initial entries in the table or does it get that from each cell of the PCV to form its base? If I supply the numbers, where do I get them from?
You should always start with a base map, preferably one close to your setup. You will find these on Power Commander's website or borrow from a buddy.
4. After a few hundred miles of using the AT, should I save those now modified cells to the PCV and disable the autotune or just let it run?
It doesn't even take that long. You can accept trims with less than 100 miles on the last "accept." After about 300-500 miles of accepting trims, you should have your A/F table dialed in. There are mixed opinions on if you should "Turn Off" the AT at that point.
5. If the autotune further improves the map/performance of the bike from when it was dynoed, why would some say no to the autotune?
Because it does and it doesn't. If you continue to ride in the same area as you formulated your tune, it continues to work just like a closed loop FI system, always making little adjustments attempting to keep it perfect. If you take your bike across country, it will continue to do this but your values will be adjusted, even if only in the allotted range (default is 20). Once you come home, figure about 50 miles if you didn't accept any trims to return to where you left.
Also, some say "No" to the AT because they are done with their mods and don't want another system on the bike that could potentially fail and leave them unable to ride. Plus, sooner or later the O2 (Lambda sensors actually) retail at $100-$150 to replace when they fail. If you don't catch it, it can also create havoc on your trim values.
6. Is the purpose of the autotune to make the bike run as close to perfect as possible in any condition because it is constantly tuning?
These are my opinions based on my research. I admit they could be incorrect based on the way I understood the information at the time. I welcome any corrections to my post.