Did you buy one of the recommended drives in Section V of the Drive Upgrade FAQ
? If not, it is possible that the drive is overheating and/or causing other components in the TiVo to overheat.
If you bought a prepared drive from Weaknees or DVRUpgrade, those drives should be fine. In that case, you might see if the problems continue over the next 48-72 hours, once the latest software is installed and all guide data is indexed. In general, TiVos are less responsive for the first 48-72 hours after guided setup, because the guide data is indexed in the background.
If the issues you are experiencing continue past 48-72 hours, I would return the drive as defective.