Sorry for the necromancy, but I joined this evening specifically to tackle this very problem, which I am also suffering: At the Performance Tuning step, getting the spinning circle on the first screen, with the Skyrim symbol and fog/smoke billowing, but never getting to that very first menu (I've waited up to 45 minutes). I'll try to give sufficient detail here in my first post.
First off, I'm absolutely amazed at the enormous effort that goes into making any one of these. Very grateful there are folks willing to put in this kind of time!
First time using a STEP guide, but I've clocked over 1000 hours in Skyrim over the years, plus thousands more in other Bethesda games, using tons of mods (back before there were mod managers!), so have a decent idea of how stuff works. Followed the guide very closely, and at the "smoke test" step, everything was nominal. The instructions said "don't run the game again until specifically instructed to do so", and that time comes at the Performance Tuning step. So I duly worked through the list of several hundred mods, installing them in sequence with the only deviations being a) cosmetic choices wholly permissible by the guidance or b) left just a couple of mods out because they didn't appeal to me, and none of those few had a color stripe indicating their requirement by one of the STEP patches.
It is my intent to try the Post-Processing section of mods, but by definition don't have any of that installed yet, because the purpose of the Performance Tuning is to establish the parameters for use in setting up ENB and LODGen. Haven't reached that stage yet. However, for the handful of mods in prior sections having options for ENB usage, I did enable those options knowing I would be trying it out. Similarly, have not run DynDOLOD etc, that too comes at a later step than PT.
There was some output I found a little confusing from the Nemesis run. The messages went by very quickly, but I saw something that ended with "all mods revert to unchecked" or something like that. I went ahead and hit Update Engine, and then Launch Nemesis Behavior Engine. I didn't understand the output from that either, seemed like error messages, but then it ended with "Behavior generation complete" as stated in the guide. Again, uncertain on these details, but it didn't look "right".
EDIT: I re-ran Nemesis just now, attaching a screengrab of the window. It shows "complete" but that sure looks like a progress bar labeled "336 animation(s)", and the little green bit just sits there, never moves, just glows and pulses. Did something get stuck inside Nemesis??
I saw that the OP here included load order, ini files etc but I'll hold off on that until/unless. Sure hope what I've got here gives someone some ideas... thanks in advance.