Currently I'm transferring a few files from one partition on my hd (ntfs) to my ext3 home directory. (nwn) I know this is going to be slow because read/write at on, so that's expected. But my system gets extremely slow and occassionally stalls for a few seconds allowing me to not do much during the process.

Another similar thing has been when opening windows for mozilla, is that if I am playing audio it will cut out and stop all of a sudden or repeat, etc. until it's done. I am pretty sure in my previous slackware la this wasn't happening and I know it doesn't occur in windows so assuming my memory isn't just gone any ideas how I can fix these kind of cpu usage problems.

Check whether DMA is switched on (used by your drives).

DMA allows the CPU to do other stuff while your DMA controller transfer the data. So, if you experience serious slowdown. Very likely, you have trouble with DMA (Direct Memory Access)

To check