If you have formated everything is good to go

Well there is one more issue

You now have an unpartitioned space (of approx 4 Gig) sitting on your HardDrive (which is not ideal - especially if it's in the first part of the HardDrive)

If you really want to confirm all is ok, then you would re-install Windows clean again, but this time remove the Partition(s) fully (during Windows innitial setup, you have this option)
And then install Windows on one Partition, being the entire drive this time (note: you do not need to manually create the partition, as Windows setup will do this for you automatically)

If you then scan for Trojans, and find none, we have confirmed that they were in the Hidden partition (somehow?) But if you do receive the Trojans again, then it must either be in the Windows setup CD, or in the Trojan remover program itself !

Basically, I don't like having un-partitioned space just sitting there doing nothing

sorry for the delay...
saturday night i re-installed the OS, and reformatted and everything, and then reinstalled Spyware doctor. Everything came up clean. I ran MBAM, and it found nothing.
So either there was something in the recovery partition, or it was a false positive...
either way, it cost my father $30

and thanks again for helping me!

Thanks for the update