Tremec makes a few trans for Mustangs. They make the T-5, T-45, T3550, TKO, T-3650 and T-56.
Tremec bought Borg Warner in 1997/1998 so ever since then all BW designs have been transfered to tremec and their name is on it. BW designed the t-5, t-45, T56 before selling it all to Tremec.
Your '99 has a Tremec T-45, V6 Mustangs come with a Tremec t-5. 2001+ GT's come with a Tremec T-3650