Heres your main problem:
What answers? I see no specific advice anywhere. Bitrate to low? Chroma upsampling? Well then why doesn't someone specifically state what bitrate should be used and how to correct the chroma upsampling?
I have a problem with chroma upsampling apparently... ...Can anyone give some instructions for how to fix the upsampling?
I was hoping that I could get advise/help from some fansub groups on this matter since they have so much experience encoding anime.
Two days is hardly any time at all to read, think, experiment... you just can't expect this sort of thing to come out right straight away, because it's a complicated process. You're spending way too much time on forums asking people to lead you by the hand, when in actuality it's just about impossible for them to know the exact right settings and fixes without experimenting themselves.
You gotta take the time to play around and read around on your own, and when you come back with more specific questions, people will be better equipped to help you and you will be better equipped to understand the answers. If you want Exiled Destiny to do it for you, leech their rips, it's cool, thats why they made them. If you want to do it yourself, you have to be prepared to put in some effort.
I don't mean this in any sort of harsh way. You've had so much advice in the last few days that I am absolutely certain that you can't have researched and fully tested even a fraction of it. If you can't get the tools you've got to work, try others. Play with some other video. I would suggest getting a handle on the encoding, then move on to the rip itself. See every failure as another lesson, and when the hard-work (reading the boring stuff) is getting too much, have some fun with it - just do whatever the hell you feel like and see what happens.