Key fob remote will not program

Okay, I have a 99' New Beetle 2.0. The key fob stopped working around March. And I had an issue with my locks whenever I locked the doors manually. Whenever I locked it, the interior door lock switches would stop working, in order to fix I had to take fuse 38 out and put it back in. I eventually replaced both door harnesses and now that issue is fixed. The key fob still will not set. I can unlock and lock the car manually with zero problems. I tried using the instructions in the owners manual and every other set of instructions I have found online with no luck. I have tried a new CCM, new fob batteries, new door latches, and multiple remotes. I do not have vcds, but I do have a VAG scanner and there are no faults in the ccm. Its really hard to explain, I will take a video and post it asap. Also, all replacement parts had the SAME part numbers. Please help me get this sorted! Its very frustrating!