You do not flush the compressor in the way you do the rest of the system...
You just empty it of oil and put new oil in and turn a few times by hand, empty and repeat a few more times... then seal it up until ready to install...
Use Brand New oil for the flush... something like Castrol Refrigeration Oil ...

That venturi vacuum pump.... is that one which uses a compressor to provide the vacuum ?
If yes, that is not sufficient to boil off the moisture from your system...

The proper kind can be rented from most rental places...you only need it a couple of days at most... if you have your ducks lined up at the start...