Ok here's an update so that maybe it will help others if they have issues:
Don't use EaseUS Todo Backup to do your cloning. I tried it again and verified that it doesn't create the service partition correctly which makes the C partition misaligned.
I ended up using Macrium Reflect to clone and it did it perfectly.
Now the bad part was, I was still maxing out at around 370MB/s reads. I went through the process of hunting down and updating all my drivers with unofficial updates and still saw no improvement.
Finally, at one point I went into the BIOS just to verify there wasn't some setting I had wrong. I already knew I had AHCI set, but after some digging, I found that my motherboard has 2 different types of 6GB SATA 3 chips. One is ASMedia 106x and the other is Intel Rapid Store. I had all my drives hooked to the ASMedia which share the workload on the chip (and are apparently overall just slower in general). I hadn't realized this prior because my previous SSD wasn't that fast so I wasn't missing any performance. It had always been wrong because I had not realized that on the board the 6GB ports are all red, while the 2GB are black...what they didn't mark clearly is that only 2 of the red ports were the faster Intel ports, and the other 4 red were the ASMedia.
After switching them around and booting up I am now getting my full ~520MB/s read speeds!
Fun times lol.