I have heard that Doug's tool is very difficult to use so I figure this patch to the source code might make things easier. PT8Sceptile created this for the purpose of AAMS's five new Pokemon which I can personally confirm are working very well, but you guys might find it useful as well. Retyping the whole thing would be silly so I'll just link:
The first post is instructions whereas the second two are those entire files in modified form so that anyone could use it even if they have no competence in programming. Indeed I hope anyone uses it; this doesn't have to just be for Doug which is why I posted it in public. Any one of you could run a server to test a custom Pokemon concept and could then post about the results here to further your efforts to design Pokemon that are just right. There are only two problems as of right now:
This method doesn't account for weight, but a server host can easily fix this. The server files contain a text file for masses for all Pokemon, and the host just needs to append the information for any new Pokemon to the end. Do note that the masses must be in kilograms, not pounds.
This method also doesn't include sprites, and I know the CAP project is famous for its well drawn sprites. Sadly the AAMS Pokemon don't have sprites (though as of yesterday, all Pokemon without sprites display the RSE Missingno. sprite, courtesy of Colin). We don't have a way to deal with this, but I'm sure Doug has some method he has been using and can post here so we'll have a complete guide on how anyone can make a server with custom Pokemon. Even if he decides not to share, the issue is 100% aesthetic and has no impact on real battles.
I hope the CAP project finds this helpful; having a free method to add Pokemon to a server should be a great boon to all Pokemon creation projects.