Best thing to do to check your system is to follow the instructions here and post a HijackThis log; we'll be happy to check it for you:

VDr's HijackThis Forum Directions

Good question regarding the download interruption; sorry I can't answer that one. Perhaps Juno has a customer service contact, or a forum where you could inquire. There may also be a setting you could change - three hours seems awfully arbitrary. If you can't get a satisfactory answer, M$ may provide SP3 on CD or someone you know might do so.