I mostly figured this one out with some help from Universal Audio support staff and Sweetwater's help pages. In case anyone else is having similar problems, try the following and let me know if it worked:
1) Check your system's DPC Latency and fix it by disabling key devices, at least while running Thunderbolt audio applications. For me, the key devices were the ACPI battery and the Realtek audio drivers. For you, it may be slightly different. Here is the step by step guide:
https://www.sweetwater.com/sweetcare/articles/solving-dpc-latency-issues/
2) Make other PC Optimizations for audio. There are a lot of system settings you should change, like power management and sleep settings, updating drivers manually (because Windows 10 updates are not adequate), admin settings, processor scheduling, etc. Just follow this guide as closely as possible:
https://www.sweetwater.com/sweetcare/articles/pc-optimization-guide-for-windows-10/
3) Disable Intel TurboBoost and SpeedStep settings in BIOS. CPU throttling, in addition to DPC Latency, can create noises like pops and clicks. There are multiple options:
http://www.geeks3d.com/20170213/how-to-disable-intel-turbo-boost-technology-on-a-notebook/
4) Disable onboard audio cards because you will be using your external audio device as your audio card. Experiment with different ASIO buffer sizes in your audio interface software, depending on how many processing plugins or audio files you are working with.
NOTE:
The steps above mostly solved my problems, but I still have some occasional noise when bypassing on/off plugins that are authorized by iLok USB dongle or when an external USB drive is attached. There is something about USB connections creating interference with Thunderbolt audio. Anyone have thoughts or suggestions on this? It is only occasional and nothing like the noise I had earlier.