You are experiencing 2 irregular behaviors:
...found in the BIOS that the old MOB would not see the HardDrive all the time (once in a while)...
...CD/ DVD, at times it starts but then stops...
I may be wrong, but since you already changed your HDD and your motherboard, then that sounds like a power supply problem. You can test your power outlet with a simple tester if you have one. But your system's power supply is not so simple to test at home. Either take it to a technician for testing, or buy a new (good and adequate) one.
Since the link you posted is not working for me, I can't take into account any of the other things you mentioned.