The center of the upper tree also has to have .250" milled down to get the upper and lower tree distance from each other correct. This will basically make the surface even with the rest of the rougher looking surface. You will also have to grind the top of the neck smooth. This is the only way to get the tins to line up with the upper and lower trees.
This is much easier on 2005 and older, but it can be done. My front end is a complete 2012 FLSTC on my 2008.