i have never heard of a system flush for an AC system, so i am not sure what to say about that. typically i just blow clean dry air through the system in the reverse direction from normal freon flow.
if you are replacing the compressor because it failed, make sure to also remove the expansion orifice and check that the screen is not packed with shavings and debris. again, you can just blow compressed air over the unit in the reverse direction.
as tkingsbury says, replace the dryer also.
finally, make sure to keep the vacuum pump on the system, once reassembled, for at least one hour, to make sure all moisture is "boiled" off. you will know when it has been long enough by whether or not the system will hold the vacuum for 30 minutes after all valves are closed.
good luck,
jim