Hi so I have a 99 with a 2.5L automatic I recently replaced the flex plate and torque converter due to cracks on my old flex plate. Once I finished my truck would not start. Now my engine wont turn at all like its hydro locked or something. I need help!! The out put shaft of the transmission spins freely when I put it in neutral but that's about all I can get anything to do.

 

Best suggestion is to pull out 1 spark plug from each cylinder, to see if it is a "hydro-lock"

Have you ever installed an automatic transmission to an engine before?

You need to install the torque converter on the transmission FIRST, you spin it and push in, the torque converter will "click in" 2 or 3 times and slide in further as it lines up with input shaft and main pump inside the transmission
THEN you push transmission forward to line bellhousing holes with engine holes, and it should sit flushes to engine, you should NEVER have to force bellhousing to mate with engine, that would mean the shafts are NOT aligned, if you did have to force it by tightening bolts then transmission has be damaged inside
Once bellhousing is attached to the engine you can then pull torque converter forward a bit to bolt it to the flexplate

Short video here on seating a torque converter, its the same for all automatics, not a Ford thing: