I've always thought of adding molex connectors as another possible point of failure, so I do splices the solder/heat shrink tube way. If you go with a molex connector, I'd make sure it was supported somehow and not bearing the full load of the bunch of wires hanging down into the cabinet.
As for J1-J3 at the rectifier board, the "Transformer Schematic" for Meteor shows the proper wire colors. It's on page 14 of the schematics pdf on IPDB.
--Luke