I would try changing the motherboard battery. Bit of along shot (nothing in your post indicates that this is definitely the problem), but the long boot time could be down to the BIOS configuation information being lost due to a flat battery. Most modern PCs will autodetect the hard disk etc. on boot up, if the BISO configuration has been lost, but this may take time while it tries all the configurations it knows about.
The age of the machine suggests that the battey could well be flat.