When I did mine, I followed the steps, reset the APM (I think, recalling from memory) in the middle as specified, and continued on. Reaching into my technical background, changes to code aren't reliant upon each other to function while making the changes, but until you get to the end and click that final "write", it may give a ton of errors because it's trying to do a thing that cannot be accomplished. You're writing to individual banks of memory, 'chips', whatever you want to call them. They all do a certain function. Changing them individually and then they work in unison together once the final result is completed.
I've long thought that the most simplistic way to do this for someone who is not experienced in FORScan, code, Hex, etc, is for someone that has completed this modification successfully to upload (I could even do it and have suggested it in the past for other modifications to both the Raptor and the Mustang) what I call "known good" ABD values that work correctly in my truck, for instance, and simply replace yours with mine. Would recommend having either exact build or similar build values, though being the Raptor only comes with one style of headlight - I'd venture a guess that those would all be the same no matter the other options.