the only thing that you should need to replace when you are doing the shift kit is the tranny filter and gasket. you want to drain the complete tranny of fluid, including the converter, and refill with mercon 5. i have an aod as well, though i used the baumann kit, and i switched to mercon 5 with no problems as of yet. everything else should be included with the kit. good luck.
2003 Ford Expedition: 5.4L, harley supercharger, 2.93 upper pulley, 4lb lower pulley, c&l plenum, jlp cai, LFP SBTB, FTSP, Magnaflow 3" catback, Eclipse AVN-5510, white face gauges, cobalt c2 boost gauge, ddm hid's, 379 rwhp, 465 rwtq sold 11/3/12
2009 Ford Flex Limited AWD