anti-theft system : car will turn over but no start. code came up as anti theft--- new module, new keys/code? Is this a fairly common problem on a 99 stang ( 178klm's)?

Take it to the dealer as you were advised. Perhaps the new module was not properly programmed with the VIN before being installed, or perhaps the module was not set up to use the anti-theft keys, and so is responding like your keys are unknown to it. At any rate, it sounds like a BCM or ignition module problem. Have your keys reprogrammed at the same time.

my 98 mustang had no problems starting since i got it 4 years ago. In the last 6 mos i replaced flex plate had to drop tranny. Put tranny back in and back together car started and fired right up. Then with in the last month started went out so I disconnected battery terminals sop to remove starter. Terminals stayed disconnected for 3 weeks or more before i got a new starter and put it in tried to turn key and got nothing no sound no click no crank no start but could bypass ignition by touching starter silenoid then i got crank to start y?