5.4l S/C junkyard swaps are going for 2500-5500.00 If I chose to purchase the complete motor I know it will drop in, but what will be involved in making it work with my 4R70W?
bellhousing difference? , what computer setup will be required?

 

This is just a theory, but you MIGHT be able to get it to work by running both PCMs in parallel. The Lightning one handling the engine, while your 4.6 one handling the 4R70W. Piggybacking like this is how certain 'stubborn' cars like the 3-rotor Eunos Cosmo can be introduced to a Haltech and still make its automatic transmission work correctly.