METASEQUOIA PMX PLUGIN SOFTWARE
However, the software can be used without knowing any Japanese) Do not use the editors if you can't understand these terms correctly (the original is in Japanese.Any changes to this usage clause affect each and every version of PMDE and PMXE.This usage clause is subject to change without any warning or notice.Do not use the editors for any prohibited usage below.Do not use the editors if you don't agree with the terms descripted below.
I do recommend you to fix those first BEFORE start worring about stuff like an MMD models or so. Taylor while I have already replied to many of your questions here, I see you are focusing now on aesthetical aspects of your UTAULOID and you have not shown us your problems regarding the oto.ini. In that case you also need to contact the author of the model to ask permission of redistributing your edit (yet some rules may say explicitly that are not permited to redistribute).
Another option is vía MME (MikuMikuEdit) to edit a existing model with pre-made pieces yet you have to know that EVERYMODEL have their rules and restrictions and editing a model, even if it's from your character, does not give you total ownage at all since the pieces/base are from others. Users like Yesi-chan (Author of Camila Melodía) and Yuma (Author of Kemonone Row) have made models with this program. Metasequoia is a good Freeware/Shareware to make 3D modeling if you want to start your project from 0.