I would follow the protocol exactly the way it is. It is important to use low fat cottage cheese. Yes you can use homemade yogurt, I do not know how well the oil will mix with it. I have never tried this so you can try and see which works better, cottage cheese or yogurt.
One thing to understand, and this is critical, is that the WHOLE purpose of the Budwig Diet is to convert oil-soluble omega-3 fatty acids into water-soluble omega-3 fatty acids.
The protocol does include flaxseed oil and freshly crushed flaxseed. I like this video explaining how to do this....
The mixture can be flavored differently every day by adding nuts, preferably organic such as pecans, almonds or walnuts (not peanuts), banana, organic cocoa, shredded coconut, pineapple (fresh) blueberries, raspberries, cinnamon, vanilla or (freshly) squeezed fruit juice. It’s usually best to place the fresh fruit on top of the completed mixture and enjoy as its own meal. Try your best to obtain organic fruit when possible. Many times this can be found frozen when not in season.
The above protocol should not be consumed with any other supplements, foods or oils at the same time. This should be a stand alone meal three to four times a day.
You must consume the Budwig mixture within 20 minutes of making it. Do NOT make more than you need and do not refrigerate the leftovers!!!
As I told you this is time consuming protocol and you must plan get the rhythm going. There were days when I did not want to do this for my dog, but I pushed myself. Sometimes my daughter helped.
This will not be a short term deal, give yourself six months.
If you are planning a fast then I would stop during the fast and pick up after fast.