For earlier 5r100w, folks are also recommending changing the pan out for a 2008 pan which allows you then to use the good filter (FT-180). The 2006 has a screen only filter and that external toilet paper roll. When the external filter gets clogged, it just bypasses it. In reality, the 2006 only filters about 10% of the fluid. If you change the pan and put in the better filter, you will filter 100% fluid. If you don't do that, there is an aftermarket external filter that is supposed to be much better than the Ford toilet paper roll.
http://www.powerstroke.org/forum/6-0l-performance-parts-discussion/1075009-08-trans-pan-filter-upgrade-quick-summary.html
http://www.filtranllc.com/home/documents/ProductNewsBulletin-TheTrap-030508.pdf
https://www.amazon.com/dp/B072J77ZG9/?coliid=I20PXS4DC4LLXR&colid=13FBUULZXH8RH&psc=0&ref_=lv_ov_lig_dp_it
