HSSS,
I'm not familiar with the TKO, but Richmond makes only one transmission for Fords and they don't use an adapter plate. Their input shaft length is 6.49 inches which is right for small blocks. For big blocks, they say you need to trim the input shaft by 0.38 inches. So, if you're not going to use the adapter plate, that would mean your input shaft should be 6.11 inches long. If you are going to use a .625 inch thick adapter plate, your input shaft would need to be 6.735 inches long. Here's a link to their dimension illustration:
http://www.richmondgear.com/01pdfs/pages25-27.pdf
By the way, my pilot bushing is flush with the crank as shown in your drawing.
Bottom line is, I wouldn't hesitate to trim the input shaft to get it to the proper length.
Chris