Wait, so you're saying you load every single aspect of the character manually? The loader lets you set up character folders so that all you have to do is navigate to them and everything loads for you. Go ahead and pop this folder into the Mods directory and see how much easier it makes everything. Just make sure you run Mods Folder.jar first.
Well, aside from my not knowing how to do it (though I recall Vanilla and the Loader had two different methods, with Loader's being deemed superior), there was also the matter that some character mods for a while came with the character codes/hairs built-in, so manually loading an "all-in-one" swf file wasn't a big deal. All of the MLP stuff is one of those times where this doesn't really apply though, as things like tails and cutie marks are done separately on top of anything else.
On the plus side, doing up mods manually made me realize some quirks I had to account for, like using the Thicker Ass 'n' Legs mod will cause the hooves on the pony body's legs to disappear, but there's a "pony shoes" mod that makes up for that slightly. As well, the pony body defaults to Light skin, which explained why some of the "show accurate" character codes didn't seem to look right when used with the mod, as the codes were made using Pale, Tan, or Dark skin as the base and the mod switches to Light without changing the HSLC settings.