engines with auto trans have a flex plate connecting the engine to the torque converter.
engines with manual trans have a fly wheel and clutch.
they are two completely different things serving a very similar purpose.
but they are easy to swap back and forth as needed since the engines, the bell housings and the crank shaft are the same.
just swap everything from your engine over to the new one, bolts included.
the car will run fine with out the EGR, but in some states you can not pass inspection with a CEL.
it has been a while since i read the entire thread, but there is a lot of good info in the one below. after you read through it ask about what you do not understand.