Upgrading from a C6 Dual-Range Automatic in a V8-460-powered F-Series is usually complicated. The E4OD four-speed automatic is a computer-controlled gearbox and will require retrofitting considerable amounts of electronics; I'm not certain, as of 1 December 2009, whether the ATS Select-Shift standalone TCM for the E4OD and 4R100-W (mfd. by Advanced Turbo Systems, Inc.) is still in production. The 5R110-W is unsupported for your engine, as Ford Motor Company went to the SAE #1 bellhousing for compatibility with the International VT365 and VT395 V8's (as well as the Triton V10), whereas the Lima big-block uses a peaked bellhousing bolt pattern inherited from the Ford-Edsel big blocks.
A better bet would be a stick-shift retrofit, which requires almost no alterations to your harnesses. As I understand things, the F-Series used the same clutch- and brake-pedal sets from 1972 through 1996 production across the F100-F350 (plus the 1991-96 F-Super Duty). In the F-150, your 460 Lima will probably require a 30# flywheel and 11" Long-style clutch (after Long Machine & Tool Co.) to fit the New Process 435 or New Venture 4500. The NP435 and NVG4500 use the same four-bolt mount and will fit your engine with either the stock aluminum or Lakewood/Mr. Gasket hydroformed steel bellhousing for 351/400 Michigan and 429/460 Lima engines. (A hybrid ZF S6-650 with the GM case and Ford input gear would be the best bet for a six-speed retrofit; however, appropriate bellhousings are not yet to market.)
