This is a guide to convert any PCC format mods into mesh .mods that replace individual outfits/hair/etc., instead of the entire file.
I'm going to use the N7 Leather Jacket for Femshep made by firemadeflesh on tumblr as an example.
In this example, when you download the mod, you have 2 files:
The PCC which contains all the clothing in the game for Femshep
and the tpf which has the modded textures for the outfit you are installing.
1. Open the PCC in Meshplorer
Find the modded outfit. All we're doing here is marking down it's ID number.
(here it is 1633)
2. Open the same PCC in PCC Editor 2.0
In the list find the ID number you marked down in Meshplorer.
Select it on the left and in the Modmaking menu select 'Create Binary Replace Job from Object' - a 'done' window will pop up.
You can close PCC Editor 2.0.
3. Open Mod Maker.
You should see your mesh replacement job already in the window.
Now just File -> Save Jobs -> All
It will prompt you to save your .mod installer for your mesh.
Now you can run the job now, or load it later to install your outfit (or armor or hair or whatever you were converting) and it won't overwrite any of the other mods you have installed already (unless it's replacing the same slot.)
TO INSTALL THE TEXTURES
You can either use the tpf with Texmod as intended, or install the textures permanently using TPF Tool. Ottemis has a detailed guide on TPF Tools here.
In the case of the Nilin N7 Leather Jacket, only 1 of the textures of the 4 is in the correct format for the game files, so to permanently install I had to do some extra changes to them in Photoshop, but that is beyond the scope of this tut! Hopefully the mod you are attempting to convert has textures already in the correct format to install.