Custom Player Model makes me go about 1/2 into the ground?

Hello! It's been 3 long months since I've ever got on to Roblox and started scripting. I am back, however, and I now have a new question!

I have figured out how to use DaMrNelson's custom character plug-in, but the problem is, every time I load the character into the world itself, the feet are 1/2 into the ground and I am annoyed. One solution I have, however, is to add another invisible layer on top of the actual ground, thus making it seem like I'm not clipping the ground. I have Motor6D's everywhere needed as well as the HumanoidRootPart and I have all of the needed components named such as Left Leg and Right Leg. I do, however, have extra parts such as knees, shoulders, etc. What do I have to do in order for the clipping to stop? Would I have to instead, name it something else and script the animations by hand or is there something I'm missing?

Note: The only thing giving the player the custom model is a script that changes out the player's character with their own. I know it's not the cause since changing the name of the legs does stop the clipping, but in return, makes me unable to jump.