Take it into Kragen or Autozone and have the charging system checked. Rule out the charging system first. If it checks out find, it may be your fuel system. Could be a fuel pump problem.
There can be a number of reasons why you are having starting problems. I woud discribe everything, but I don't have time to break it all down. But, start with the charging system (battery & alternator).
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'99 Duratec SVT 24v V6
-Cold Air Intake/Diablo Chip/4" Bomz Muffler/Bosch Platnium +4's/HO alternator/Dual Oil catch Cans/UDP/Goodyear Eagle GT tires
Asethetics-Carbon fiber Ford emblems/SVT engine & tail emblem/SVT High Output fender emblems/Mesh upper & lower grill/hood protector
-MACH 200 watt stereo system & 800 watts of power on my 12" MTX speaker box w/1 Farad Monster Cap.