Update: So, I purchased Gelid GC-extreme thermal paste and finally got around to applying it! I feel like paste on the bottom CPU got smudged a little bit when I tried replacing it; however, the top one was fine, and I think both are okay altogether. I let it sit overnight (as I had other things to perform on this machine the next day) and fired it up recently. It began at 90F and climbed up to 97F at idle. I then performed a few small tasks and it went up to 100F (this all being for CPU A). Now, I am currently browsing MacRumors (which is a very heavy site nowadays), and it's up to 108F. Now, while I have seen some improvements, I feel as though they still may be just a bit higher than they originally were from the start. That being said, it is a little bit warm and stuff in my room. The machine is having a little bit less airflow than before, so it may just be at this temperature because of that. I'll continue looking around and making sure everything is fine with it.
Currently, though, I am a bit more satisfied.