Okay, I found some answers to my own questions. I'll post the answers here so that if anyone else has these same questions in the future hopefully this can help!

1. After consuming the cottage cheese/flax oil how long do I need to wait before eating?

ANSWER: depends on whether the full Budwig Protocol is being followed. If fruits and veggies are the next meal, then waiting around 30 minutes is preferred, although an hour is better.

2. How long after consuming a regular meal do I need to wait before consuming cottage cheese/flax oil?

ANSWER: 1-2 hours

3. I am currently using organic cottage cheese (6 tablespoons) to which I add 3 tablespoons of Barleans Cold processed flax oil. Do I need to add ground flax seeds to this mixture? I'm unclear from the instructions if I add both flax oil and ground flax seeds.

ANSWER: some say it is required to grind flax seeds and add to the mix at least a little bit, others say a good cold-processed flax oil of high quality is sufficient.

4. Do I have to use a blender? or is it sufficient to mix it thoroughly with a fork?

ANSWER: a blender or mixer is required as a fork will not mix the substances effectively.

5. Is there any problem eating the cottage cheese/flax oil mixture right before bedtime?

ANSWER: apparently Dr. Budwig didn't recommend eating the mixture right before bedtime.