I got in contact with Pocket NC's support team, they suggested another possible solution. That was to recalibrate the tool setup, which required manually finding how far the z-axis tool traveled and then offset it with a 123 gauge block. I didn't have a steel 123 block, so I used a piece of wood, cut it down to roughly 3" making sure all the faces whereas square as they could be, and then used a pair of calipers to find the exact thickness. Using wood is not the most precise way of doing this, and I am well aware of that, I just needed to come close enough to find out if the tutorial would get close enough.
I then followed the tutorial and had similar results as before, which was frustrating. Since it kept measuring consistent results, I decided to try once again and find how far it was off by dividing it by two to account for both sides and adding that to the tool offset measurement. I was shocked to see that it worked! It measured out to 1.0015," and the 3D design measured 1.0", 0.0015" off wasn't too bad and was an acceptable tolerance. I then faced another side of the cube to make sure it was consistent, and I got 0.9980," which was 0.002" off, also an acceptable tolerance.
I then reverse-engineered this into an equation I could use for inserting other tools. The previous equation was -(3.6-tool length)= TLO tool length offset; with the new equation, I got -(3.573-tool length)= TLO. I had to confirm then this equation would work for other tools and get consistent results. I inserted a new endmill, measured it, and input the information into my equation and got near identical results. I was delighted with this outcome, and now all I need to test is the b-table offset and make sure that it is consistent and accurate. I didn't have enough time to cut another cube, so it would have to wait until next time to do more extensive testing.