The arrow on the drier should be facing the evaporator coil. Usually the lines on the micron gauge means the system is not under a deep enough vacuum to read yet(usually above 12,000 microns). How long did you have it on a vacuum before shutting down?
Ok, I take it the lines were open since they were cut. My worry would be that they are filled with water or something that may have gotten into them. Did you try blowing nitrogen through them or do a pressure test after re-connecting them?