[rspencer]

...if a transfer that is currently inactive on the tracker was re-done from scratch does that person need to select the reseed button while uploading the new one

No, a reseed would have to be the exact files as seeded before.

...or just create it and mention that it is a fresh new transfer/mastering job.

This would be the way to go.

Also if one is currently active does that person request that the first one get pulled due to the new transfer being better due to using a better A/D converter and mastering techniques.

Provided that the person seeding the new transfer is the same as the seeder of the active torrent, yes, just report the old torrent & let us know.