Right. So. Using Mod Organizer 2 to try and get a modding set-up working, after Vortex proved a poor choice. Complete re-install and even cleaned out certain folders of old .esps that'd been kicking around. Current mods I have installed are:
FNV Mod Limit Fix
NVTF - New Vegas Tick Fixer
Manual install of d3dx9_38.dll and .tmp from the New Vegas Heap Replacer (console doesn't open on startup, which makes me think it was unsuccessful)
JIP LN NVSE Plugin
Yukichigai Unofficial Patch - YUP 12.0
Unofficial Patch NVSE Plus
Project NEVADA DLC Support
My Fallout NV is 4GB patched via the last update of Roy's old patcher.
PN is there mostly because I know it's going to end up high in the load order and was one of the first mods I wanted to get locked in, but doesn't seem to affect this issue. Even with it's .esms and .esps disabled, the issue remains. The issue being: debilitating slowness/cursor and game lag. Seems to be on a very core level, as Doc Mitchell's walking animation plays in an odd, stuttering sort of fashion and his lip-sync is way off. Toggling ENBs effects on and off via the default keybind seems to have no affect on the issue. The lag is present from start-up, as even before a save is loaded, the opening slides even have frame issues (trust me, it's not just them loading slow, it's visually noticeable) and the cursor jumps all over the place.
I've tried adjusting a number of things in enblocal.ini to see if it'd have any affect, but nothing so far has produced even the slightest difference. Neither the expandsystem memory stuff or the 'unsafe' memory hacks. As well as inspecting FalloutPrefs to make sure the multisample and waterdisplacement values are set to 0. HDR is enabled in the launcher, AA is disabled. I've done all the recommended things and checked and double-checked all these different .ini's. I feel like the issue is something I'm not thinking to check, or that's screwed up on a very basic level. Oddly, before this, when I was using Vortex, with a wildly outdated half-install of NVSE and a malfunctioning ENB setup leftover from years ago, it ran like butter with significantly more mods installed, despite some clear issues with the game itself caused by conflicts and/or load order, most likely, so I'm really at a loss. Hence why I turn to the forums, here.
Any help in sleuthing out what's wrong here would be massively appreciated, as I can tell if I can fix this I'll have a solid base to work off, with the more methodical approach I'm trying to take and MO2's more direct controls over things.