It's done.
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Hope you like it. 18 leechers appeared in the first five minutes LOL 
So you didn't split it individually. Got chapters?
Yes. Episodes are identified with chapters. Also each episode has chapters for Intro, OP, Part 1, Part 2, ED and Next Ep.

I couldn't split the mkvs with mkvmerge. It didn't cut the video at the exact time I entered. I still don't know why. I also tried splitting in only two parts at a time but it was the same. For example, if I put the splitting time at 1:32:43 mkvmerge cuts at 1:32:13.
So, this is a reply to a really old post right here. I found out what was going wrong. You need to split on an I frame in order for the split to work properly. To find it, open the video in AVSP using FFMPEGSource, go to the time you want the split, and then hit the right or left arrow keys until you get to the first frame of part 2. Copy the time exactly as it is show.
Put that time as the split time in mkvmerge in full. So, do 1:32:43.024 or whatever it is. This will split it exactly at that time.