I suggest joining all the sections together as previously suggested and encoding them in one run. Doing it as a single video is more optimal than lots of little bits because the codec can pick and choose more carefully, and also it gives ratecontrol more to work with. If you are struggling with some areas, use zones in x264, it's not ideal, but it's a lot better than encoding parts and storing them in a non standard container IMHO.
Basically what you are doing is taking a jpg that needs 600KB and trying to get it to 100KB and it's not working. Not being happy with the result you cut the image up into parts and save them at different qualities to reach 100KB, it may look better in parts, but it's inconsistant.
If for some reason you were encoding parts so people could skip to them, well in MP4 you can encode a single stream and just make a chapter file.
Also, I know I sound like a broken record, but you really need to forget bitrate and filesizes so much if you are hell bent on reaching a certain quality. No matter how hard you try, some videos just have to be larger than you would have liked. Sometimes it's like trying to fit an elephant into a mini cooper. It just won't happen without getting ugly or losing something. My final advice on the matter would be that sometimes you can over analyze things, especially with AMVs where you aren't talking about huge filesizes to begin with. Personally I would really stick between QP18-20 or CRF 18-20 with maxed out settings (as my previous post) and just live with it. Anything beyond CRF20 will start to get ugly, and if you still can't reach your target at CRF20, then so be it; the video simply requires that filesize for a good, consistant quality.
I hate to sound pushy, but really I think you are spending more time on this than practicable for megabytes, I'm just trying to save you time here
Of course it's great that you are willing to try these things and experiment, so I shouldn't discourage you at the same time.
Nice vid by the way
