Thanks for the insight everyone. I was planning on doing a rinse or two of the fish prior to introduction to the DT just to make every effort to mitigate any possible Cu contamination. My main concern was if there would be any adverse effects to the fish transferring from the Cu water in QT to the Cu free water of the DT. Also, I try as much as possible to never use a net; I will either always use my hand or Tupperware container to catch/transfer fish, that's just my preference.
As far as the bacterial population is concerned, I have been ghost feeding the tank since fallow. Recently, I have stepped up the feeding regime knowing I was going to be reintroduction a larger bioload than the tank was used to for the 13 weeks fallow trying to build up the amount of bacteria. In addition to this increased feeding, my plan was to slowly reintroduce the fish over the course of a week to a week and half rather than all at once (this has the added benefit of letting the more timid fish reestablish a territory/area). The end of the Cupramine treatment is not until the 20th so I still have 11 days to further attempt to increase the bacterial population.
Concerning the treatment time, I do not have my QT record book with me at work so I am a little fuzzy on the exact dates, but the fish have been in varying levels of Cupramine since the end of January. I was originally planning on doing 4-6 weeks Cupramine treatment then moving the fish to an intermediate, larger holding tank while the DT remained fallow for 12 weeks. The 13 weeks came into play because of external circumstance I did not test the Cu levels in the QT for a while and 3 weeks out from reintroduction to the DT I noticed a possible ich spot on one of my clowns, however there was no indication on any of the other fish or flashing/quick respiration to indicate ich contamination but better safe than sorry so I retested the water in both QT tanks and they were 0.27 and 0.30 Cu. I decided to redose up to around 0.45 keep at that level for 4 weeks. This would only add an extra week to the whole process and frankly I'd rather stare at a fishless DT for one more week than do this all over again.
So thanks for the help and as always any additional information or critique is always welcome.