Mac Pro Mouse Lagging and Sound Skipping

My Mac Pro 1's mouse is lagging and the sound is stuttering.
I took it into the Apple store and they ran all the tests and had it pinned to a RAM issue and a graphics card issue.
I upgraded the graphics card to the ATI Radeon 5770 and upgraded the RAM then. It has a new hard drive in it, and is running snow leopard as well. All of this has improved it, but it is still creating the same problems.
What is left to be done?

You should absolutely contact Apple immediately. This does not sound like trivial problem and is probably indicative of an imminent total failure.
Mac Pro 2.66; 1 GB RAM (until price drops from heavenly highs )   Mac OS X (10.4.8)  

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