05 can be tuned pretty easily with HPT, later years have no tuning support IIRC.

I would say just tune out the DOD, trying to swap the entire valve train ends up to be more hassle than its worth.

For the transmission, look up Triple Edge Performance, send an email to Dave there and he'll get you set on the right path. His built transmissions are the best you can probably ever get... They're worth the price.