First off I would consider reposting this in a manner that will get answers that are directly related to your original questions. Don nailed it pretty accurately being concerned with the vast amounts of parts recommended for your project. I will also admit to knowing next to nothing except what I have learned from this forum for the past 5 years or so. Like many others on this site I know a number of people that earn a living on these bikes while employed at either a HD dealerships, independent shops and high performance shops. From what I have read here or been told & seen first hand from professionals I know I would expect to see a new or slightly used T/C motor with more than the .003 or .004 run out. This was posted as causing a major concern. I know he is right being concerned but I believe more bikes are over .003 than under and that is counting the new ones. I have two nephews (twins) that each purchased Road Glide last summer with the 103' motor. They ride real easy and each bike had less than 5K miles. One is a car mechanic and decided to do a similar project that you are planning on both bikes. One run out was .005 and one was .0075. My 08 just happens to be close to 11, so its needs to be addressed. I agree that it is excessive but it is also normal in the HD world and they won't touch it until it is out to 12 I believe. No intention of stirring the pot only stating facts as I know them, high run out is much more common than people are led to believe and that is real unfortunate and quite possibly unnecessary by HD.
Good Luck