first good choice on the megasquirt next you can connect them via USB with a serial USB converter.
yes you can use the hard drive although it might be a bit small
Yes you could use the mobo if you got a new one but you need to watch the power it will take and work out your power supply. depending on the chip form factor you might be as well getting a new board and chip or go mini ITX and be much smaller.
CD/DVD isnt worth using as they arent meant to be used on the move so will jump a lot and probably damage disks. Much better to use a slimline laptop drive the extra bonus being they use less power too.