That system does not meet minimum requirements. Get a system that does better than minimum requirements for that material.
As HARM hinted; you will have significant problems with everything on one harddrive. Partitions do nothing to help performance; they are for visual organization only. You need a minimun, of two fast harrddrives.
Actually, partitions present themselves to the OS as physical HDD's, and the OS cannot understand why it's taking so long to get reads/writes. They are hold-overs from OS's many generations back. Other than some esoteric backup schemes, there is no reason to utilize them A program, like Partition Magic, will help rid your system of those.
I do agree that a minimum of 3 fast HDD's is the minimum for Video editing. More, properly allocated, will be better.
Now, with 6x HDD's, I have many Projects with a lot more Clips, and no issues.
You may also want to consider transcoding your MP4 videos to a more editing friendly format (such as .avi or .mov using the NTSC DV codec if your footage is SD), or using Cineform.