Try running the RAM test, described in the FAQ here. That would be one possibility of causing a lock. Also, does the lock occur on AC as well? Capturing the serial output would definitly help.

I get a clicking sound from the player, typically while there is disk activity, but not always.

Is this only when you are driving? The one drive models had the end of the cable stuck down, but it had a tendancy to become loose and could be banging against something. Also, the handle may be a bit loose, try seeing if it's a result of that vibrating away from the front of the case a bit. If the drive icon is not on (and you have it enabled), then the drive is not spun up at all, and shouldn't make any noise beyond a faint srattling sound when shaken quite a bit.

and one thing I noticed was that the right side of the hard drive holder is no longer securly mounted to the case.

I'd try to just remount the drive mount. It's the 4 screws on the left and right side that hold it in place. Be careful when doing this though, as the drive cable is tucked up against some rather fragile components on the display board, and forcing the mount out could break one off.