Okay, I was hoping I could get away with using what worked for my other computer on this one, with small modifications, despite it being a different system. I started from scratch with the above post and have successfully installed 10.14.4. Seems to be working.
However, there is one critical exception: Disk I/O seems to be off. In my Hackintosh2, I have a a WD SSD as the system disk, and a Samsung 970 Evo as a data drive for my work that requires fast I/O. On Hackintosh3 (the one that's the subject of this post, the new system), I have a Samsung 860 Evo as the SSD system disk, and the exact same 970 Evo for a data drive. Both formatted as HFS+ (though I have tried to fix this problem with formatting as APFS and it didn't change anything). Using Blackmagic Disk Speed Test, I get around 2500/2700 MB/s on the Hackintosh2, and 2300/2700 MB/s on Hackintosh3. Slightly disappointing, but I can live with it.
The issue comes when I do my benchmark for work-work. This involves reading/writing many small files (~MB) and some large files (GB) and doing stuff in RAM. On Hackintosh2, there are no issues, where the test runs as expected, and iStat Menus shows all 12 cores running and roughly 95% user 5% system. However, on Hackintosh3, I get stuck and instead of 36 cores going full-blast, I end up running at 55% capacity, with 30% taken up by the system doing ... something? (Activity Monitor doesn't say) and only 15% seemingly running my code during the most parallelized parts. The disk I/O for these tests is MINIMAL and doesn't come anywhere close to the limit (like, by a factor of 100x).
I thought it might be because it's 36 cores versus 12, but that's not the case: I then moved my files to the SSD instead of the NVMe. The same test ran in 2/3 the time on the SSD as on the NVMe on the same system. It STILL took about 15% longer than on my system at work, and some parts still went down to 30% system 15% user, but only in some areas of my code (despite the exact same steps using 100% about 20 minutes earlier). I'm also not hitting a thermal limit, for I took off the OC and it's running at stock speed and capping out at 65°C. (Note: The same system at work (same motherboard, CPU, and SSD/NVMe) runs these work benchmarks more quickly with Unix as the OS. It's a mixture of Python and code written by the US Geologic Survey.)
I also checked the quoted X299 install guide and made sure the SSD/NVMe TRIM Support kext to patch is enabled, and it is, and I've tried restarting.
Any ideas? I built this system primarily to run this code at this point in time, so if I have to, I'll reformat everything and install Unix, but I'd greatly prefer not to.