It would be a good idea to grease all areas that require grease to roll smoothly.

I believe Non-Fixie was saying not to remove the fixed, drive side cup when re greasing the bottom bracket.

Good idea to arrest the rust on the frame. Many ways to accomplish this. Best to research and decide for yourself which method you prefer.

nice thing to have Flandria on the rims. Keep those but get yourself a set of aluminum wheels.