Im not an expert. From what I understand in 1999 ford took the 4 speed auto and made a 5 speed. They did this with some electronic trickery. By creating an intermediate gear between 1 and 3 gears. I read this years ago from popular mechanics, so I could be wrong. 2cnd gear is not actually a hard gear as such.
My advice is get it to a shop. It may be something as simple as a shifting solenoid or valvebody fix. Wait to long might cause clutch or band wear and damage.