Update..
Last night while working on my final project, and having the computer overheat 5 times I decided to take further action.
Previous when I was pulling it apart, I didn't pull the heatsink from the CPU because I didn't have thermal paste to reapply. In a bit of frustration I decided to pull it anyways. Along the edge of the heatsink that gets air from the fan there was a THICK coating of dust.
I pulled all of the dust off, and replaced everything. Since then it hasn't overheated, and the fan hasn't had to run full blast(quieter).
I used the PC about 4 hours after that.. so it's too early to tell if this has solved the problem, but it's looking promising so far.