Replaced plugs and coil packs because of several misfire codes. Ran fine for a few days then again misfire codes for cylinder 4. On inspection found water in the spark plug well. I think I had water in #3 and #4 when I changed the plugs and packs originally.

 

Which engine do you have?
Did you use Ford plugs and coils? Fords do seem to run better with Ford parts.

 

Some modular engines had issues with pressed in coolant pipes/ fittings leaking.. I am not sure your 5.4 is prone to those issues which would allow coolant to leak and collect in the plug wells but is worth looking in those areas for leaks. Water in the plug wells likely is causing the misfires.

 

Coolant is what I'm thinking as well. The 5.4 heater hoses are known to leak on the rear of the bank 1 valve cover most the coolant ends up in spark plug holes 3 & 4.
If thats the case drain the coolant, remove BOTH the heater hoses, blow out the spark plug holes throughly and dry the coils out as well, reinstall coils, replace BOTH heater hoses and refill the cooling system.