Decided not to meet today with Darryl since we wouldn't be ready until 3pm and this would leave us about 30-45 minutes of actual work time before I had to leave for Senior Design class. So we will just work at our respective locations individually and share any insights found with one another today.
So far I have gotten Quartus to allow me to add the desired components to the LogicLock regions window. The only issue so far is that you can't properly cascade some of the blocks since they have been instantiated in multiple .bdf files and the LL window doesn't allow for copies. I may have to rename some of the blocks if this is an issue, or LL may be smart enough to work on every instance of that block in the multiple levels it appears in.
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