Can you remove the flex plate torque converter from the blown engine of a 1999 Ford Escort ZX2 automatic in order to install a new engine with a manual transmission?

yes BE SURE TO REMOVE PILOT BEARRING IT IS PRESSD IN NEAR THE REAR SEAL it can be difficult sometimes to remove in the past i had removed pressed bearings by loading up with grease as full as possible then use a shaft that fits almost perfectly and thump it this will create hydrlic pressure and press the bearing out i

Yes you can and there is no pilot bearing,Front wheel drive transaxles do no use pilot bearings. Just remove the 4 nuts that secure the torque convertor and then the flex plate bolts.