I am working on a separate project "STEP Thunderbolt" that will take care of custom STEP installations. Basically you drop it in your mod download folder and start it up, it will rename all the files in that directory by pulling data from nexus and the step website. It will repackage all mods into a nice bain friendly file and combine mods that have many different files into one.
When you open up WB or MO for the first time after doing this it will add all of them in the correct install order and with human readable names.
It will eventually be able to download required files that it does not find in the folder (and the latest updates of files it does find). These functions won't be limited to STEP either, eventually I'll add an editor interface where you can add your own custom repack/rename data for any mods you like.
Course this is a bit of a long term project so be patient...
I've been working on Thunderbolt (the STEP installer) and learning Semantic Wiki (which is gonna be the backend for Thunderbolt) instead. I'm not gonna stop until I figure out a good system design...
Thunderbolt automates many of the tedious aspects of installing STEP properly like repacking and renaming all mod archives after they have been unpacked, cleaned, and optimized by DDSopt and TES5Edit. It will sort through independent files and grab only the ones most optimal for a STEP install so you don't have to worry about following all the STEP installation directions and each mods installation directions, kinda like TPC but even easier. It won't be out for several months and after initial release features will be added gradually until it basically does everything for you, including downloading (although you probably still have to click each mod on nexus due to legal restrictions). You will still need to use WB or MO to actually install/uninstall and BOSS to order plugins, but the mods will show up in the correct STEP install order so you just have to click each mod in order to install STEP.
Thunderbolt will eventually (in a year or 2) do much of the hard work for you but never all, the first incarnation of it will simply rename files to presort them into installation order and make them easily readable in Mod Organizer and Wrye Bash (Thunderbolt will never replace these utilities, or others like BOSS, TES5edit, DDSopt), its intended to fill in the gaps and make the installation process more seamless, nothing more.