You should be able to manually change the models you speak of using the ulgp tool. If you want to revert back to original game models, then you will have to start with a fresh install of FF7 and run Bootleg again. I don't know what settings you want to tweak, so it may or may not require manual work.
The basic thing to know is that Bootleg is an installer, not an uninstaller, so it can install and override certain things, e.g. models, textures, music, etc. when you run it again. These files are typically easier to find within the game installation folder, so manual installs can be done if you know what files you want to change and where to find them. Any of the more "picky" features do not have an easy way of uninstalling, so in those cases you would be best off starting with a fresh install and running Bootleg again.
My absolute honest advice is to always start with a fresh install and run Bootleg again. Layering a whole bunch of manual installs on top of each other, especially after Bootleg has already run, requires a lot of inventory work and is sometimes tricky to get right. That is why Bootleg was made to automate the process
