Probably the disc is a bit ruined (dirty, scratched or you used a low quality disc that after some time become difficult to read, typical of Ritek media for example).
Another possibility is that DMA is not enabled. After a fresh install it is a frequent issue. Check and enable DMA for all IDE drives drive
I also suggest to get rid of the Intel Matrix drive. It’s basically useless, and as you already noticed it causes a lot of problems.
About the Pioneer drives, bear in mind that by factory the ripping speed of these drives is locked, so if you are searching for a fast ripping drive you must unlock the drive first (this require the installation of an unofficial drive that invalidate warranty, but this has been done by hundreds of people here and it’s a safe procedure :))
Another thing you should do is check that the PSU is sufficient. Even if the E8600 is a 65W CPU, it is possible that your PSU is not enough powerful to run correctly the system.