I would replace the evaporator. They are hard to flush IMO. You will need a new receiver/dryer (don't install until you are ready for final assembly and charge), and flush the lines with a good A/C flush, although I have heard that brake parts cleaner works.
Replace the orfice tube and all O rings with ones for PAG oil. I put a little PAG oil on the O rings, but I do not know if it is right...works for me.
You can blow it out with dry nitrogen or even charge with it to check for leaks.
The condenser is the hardest to flush, so it is good that you are planning a new one anyway. Just make sure you distibute the oil throughout the system when you assemble, and pull a vacuum at least 3 times for a half hour each time, with a half hour between. I like a small cfm pump (2 or so) with a system this small.
You are correct that a new compressor will have the correct seals, but it may or may not come with oil in it.
I am going with all new parts when I do my SS. Best of luck, let us know how it comes out.