It sounds like the Mac reset the PRAM (where time, and some other settings are stored). The forst boot after this is cleared can take longer, so things on that end are probably fine now. Some things also don't like being set to the wrong time, so that can also explain some of the delays you saw. I'm not sure if Macs are still defaulting to 1904, or if they start at Unix time of 1970 ow when the clock resets.

There are a few ways you can check the disk. First, run Disk Utility and see what the S.M.A.R.T. Status in the bottom right says when the hard drive is selected. Also, open Terminal, and run dmesg to see if any disk errors are showing up there. For a more historical view, open the Console application, and choose the system.log, or archives of it under /var/log. The filter disk should reveal anything of note.

Finally, to do a full disk check, reboot off the Mac OS X install CD 1 (or DVD), and once to the first installer screen, check the menus for an option to run Disk Utility.You should then have an option to verify disk, something that is greyed out when booted to the hard disk.