Two points here. On is based, the other is to maintain a low profile from litigation..Wikipedia wrote: " Dōjinshi creators who based their materials on other creators' works normally publish in small numbers to maintain a low profile from litigation."
To create a full anime episode on existing manga would no longer be "based", it would be a copyright infringement. I am familiar with a project which is making stripe cartoons of famous films for mobile distribution - the authors have had to obtain licenses from the original film houses to be able to do this.
The "avoiding litigation" is also interesting, since its clear the guys at Comiket do risk such hazards.
Vern's suggestion of creating an original is a fair observation - you have the talent to draw the boards and put together something, why not develop something original which is yours, which might create something good for both yourself and others. It is what Hitoshi Ashinano did when he created Yokohama Kaidashi Kikō originally.
I write original films for a living - some get taken up, others get passed. Whilst getting accepted on something is great, the best part is the creative buzz about inventing new worlds and populating them. It's always an amazing discovery process, one where you are shocked or surprised by what your characters say or do. You never really know until you put them into a particular situation, the characters then 'take over'. Some stories are for kids, others for adults. All of them have turned out to be creatively rewarding. Some turned out to be workable and got optioned. One script series even got made.
Just a thought, not criticism.
Rhoel
edit:
Ewans previous reply was posted whilst I was writing this.
The fact he is pursuing the permissions thing is good to hear - he may be lucky in that he may very well get permissions to make, just because he asked. It certainly will resolve any 'down the road' issues, and prevent two people making the same episode.
