Think about it this way, a person is convicted of killing someone based on the testimony of a witness that should have been thrown out, the accused is convicted of manslaughter. The murderer appeals the case based on that tainted evidence, and an appeals court sends the case back to a lower court for retrial without the testimony from the witness. However in the mean time, the prosecution finds the gun, a video of the murder, and an unimpeachable witness saying that the accused planned the murder for weeks. The prosecution can now use this to seek first degree murder charges, something that they could not have done if the appeal by the defendant were not successful.
It sounds like the original charge was dismissed based on the search being illegal, however the government had dug up lots of new evidence in the meantime to show he was a much bigger player in drug trafficing than they could prove back when he was originally conviceted.
It sounds like these were different charges. It's also likely he would have faced them regardless of if he appealed his first conviction or not.
Probably neither. There would be issues of double jeapordy only if the conviction was reversed because of either insufficient evidence or gross prosecutorial misconduct. If it was simple error at the trial court level that caused the reversal, there should be no problem with a new trial on the old charges.
The judge is free to sentence him based upon the conviction, without reference to the earlier results which were set aside by the appelate court. (Setting aside, for purposes of this discussion, the whole issue of sentencing guidelines.)