Just to catch an easy answer first, I got to ask... on page one someone asked if you changed the spark plug wires, on page 2 you confirmed you did.... Are you 100% sure you got the firing order correct? Now that we have a phone in our pocket I take a pic before I do anything, and if it was running well put it back like original, if it was running like crap go double check the wiring order with the spec. I googled 2003 ford 3.0 and came up with exactly one order 1-4-2-5-3-6, but 4 different engines & 2 mountings (standard and transverse).... quick double check on the firing order.
(The diesel's numbering scheme is the oddball - you don't count the cylinders the same on it.)
As one of Ford's engines with a displacement that stuck for a while in different versions, the 3.0-liter V6 has been around for quite some time. The thing is
rerev.com
A
consistent misfire tends to lead me to a miswired spark plug wires.