Download the TKO parts manual here:
http://www.ttcautomotive.com/English...090110_145.pdf
Page 6 shows the exploded picture of what needs to come out.
Drain the trans and get it "nose-high" on a bench. Remove the 4 bolts holding the bearing retainer onto the front of the trans. Slowly remove the input shaft being careful not to drop any of the rollers into the case (shown in diagram). Take the shaft to a machine shop and have them mill off however much you think it needs (mine needed 1/8".) They can also bevel the end for you. You'll need a tube of Permatex Anaerobic sealant (local auto part's store) to seal the retainer back on the case.
One banana job.