Assuming everything is perfect, expect a 14.2-14.3 ET if you're a semi-experienced driver.
I'd save my money on the flows unless you have to have "the sound". An H or X pipe will help, as will an MAF.
Don't know too much about automatics, so I don't know if 3.73s or 4.10s would be better.
Maybe a shift kit?
OK, automatic owners, its time to chime in...
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"The Yellowjacket"
1998 Mustang GT
13.97@103
"Traction Impaired" or "Nitto Needy"