I have missed over two years of prayers but have kept track of every single one, so I know the exact number. Do I have to do the qadha for every single one (over 3000) and is there a particular order I have to do it in? Please tell me exactly how I would go about this.

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Yes you have yo make up every single prayer missed. You may see this video on how to make them up:

https://youtu.be/hgDq0Mm-SL8