I’m trying to transform some of these MeshParts from a roblox package in attempt to create a custom rig using Blender. The problem is once I’ve uploaded them into studio and plug in the mesh ID’s, the following occurs: 
Try messing around with the C0 and C1 of the Joint that the limb is connected to. In this case, the LeftKnee joint.
They’re backwards because they’re backwards in Blender.
They’re not aligned because mesh position in Blender has nothing to do with where the mesh will end up in the rig inside Roblox. Your rig works only through attachments. If you replaced the leg mesh just by changing the MeshId, you will get unintended results because mesh geometry is different. That most likely means the size of it is different. That means the attachments will be misplaced. And that means limb locations will also be misplaced.
Start from fixing the orientation of the meshes in Blender.
