just a shot in the dark but the clicking sound would either be heat or pressure, i wonder if somehow the fuel is being put into the cylinder after shut down and the fuel is pressurizing the cylinder and the clicking is from the pressure working its way out.???? or could you be out of time and it gives it a squirt and no spark on shutdown?? if it were me i would put a fuel pressure guage and vacuum guage and double check timing. smell you oil and see if it smells like fuel. i allso have had tfi issues that when the engine warmed up the idle would surge and engine would bog athen die alltogether. 15 mins later would start up and purrr like a kitten then............. well you get it. sorry i am a backyard mechanic and not a mustang guru but i'm finding things on my stang one prob at a time too. good luck. i really would like know what you got going on there.!!!