I'll take a look at your mod, but re reskins, see
the Civ5 tutorial. You'll need to download
Nexus Buddy 2. Feel free to ask me any questions.
EDIT: The short version: Unpack the FPKs [using the script in Nexus (part of the SDK), or
Dragon UnPACKer (a third party tool)], make copies of the .fxsxml, .gr2, and the 2 .dds files of the unit you want to reskin [in this case \common\siege04s.fxsxml, \common\siege04s.gr2, \dx11\siege04s_diff.dds, and \dx11\siege04s_sref.dds]. Rename each of the files appropriately. Open the .fxsxml in a text editor and change the references to the new filenames. Open the .gr2 in Nexus Buddy 2 and change the texture references to the new filenames. Add the 4 files to your mod [in ModBuddy], and make sure to set them VFS=true by selecting them in the Solution pane, right-clicking on the selection, and choosing Properties. Then set "Import into VFS" to True. [Note you may want to just ignore the sref dds file which provides where the unit should be shiny. If you don't need to change that aspect in your reskin, you can reuse the existing filename for the sref and not bother including a copy in your mod.]
EDIT #2: So I examined your mod. I don't have RT yet, so I'm not quite sure how the hybrid stuff works, but I'm going to assume you have done it correctly. The only issue I see is that you need to check Reload Unit System in the mod's properties [in ModBuddy].
EDIT #3: You will also want to add <UnitFlagHeightAdjust>0</UnitFlagHeightAdjust> to the ArtDefine_UnitInfos table per
this thread.