Hi Kate, as I mentioned earlier, use Eusing to clean up the registry.
To be ultra safe, create a system restore point first and the option to use the Eusing Backup facility.
In relation to the boot order, this is controlled by the BIOS software and has nothing to do with XP or whatever O/S you are using. Whilst the two may communicate to some degree on boot up, the XP system restore will have no influence on the boot order. Any changes made to the boot order has to be saved to take effect. This is normally done by pressing the F10 key and confirming the save. Any loss of the saved settings may indicate a failing motherboard battery. This is normally associated with loss of time and date settings or a default to a previous date in the distant past. Excluding a faulty motherboard battery, the fact that your hard drive was missing but later returned to the boot order may indicate a possible hard drive problem or just a dodgy bootup. Far to early to make any judgment yet so do not be overly concerned unless the problem persists, having replaced the battery.
If you are still unsure about altering and saving the BIOS settings, you can either PM me or continue in this post.