Alright, I'm going to try and not flame ya but there is a TON of information on this forum about your number 1 and 2 problems.
But if your not sure what your looking for then here's a little more info. Basically the reason why you have sound comming through your speakers is because most likely your speaker wires are close to a ground... (consider buying a ground loop isolator) or re-locating your speaker wires or ground wire.
2, the thump your getting is from your PC's sound card. There are startup controls / DC-DC regulator such as the Carnetix 1260 that have a delayed amp turn on feature... basically this turns your pc on with the ignition wait a few seconds then turns your AMP on, this will get rid of the thump.
in Response to your 3rd question... Your not touching your ignition are you ?? If so leave that alone !!! you will find an ignition wire or accessory wire that turns on with your ignition attached to your radio... use that... don't rip your ignition apart...