My house is a C.P. Morgan home that has all flex ducts ran off the plenums, supply and return, with no trunk lines. Would it be better to run the trunk lines off the stacks or can I get adequate airflow without doing all that work and money. I already got all of my sizing off the Manual J and D. Any tips on doing them to save a little dough... especially the returns? Should I insulate the ducts... they are in the attic.

If you by flexduct that is already insulated than no you don't need to reinsulate them. I would get a higher rated insulated duct to do the job since you are installing in an attic.

I forgot to say that I was thinking about running all new trunk lines for supply and return along length of house. I don't know how much better this would help the air flow rather than long spans of flex.

All duct in a unconditioned attic space has to be insulated by code and the more insulation the better. There are different classes of flex duct and I suggest you buy the highest R value available. I have successfully installed systems using flex duct only but the instructions must be followed exactly of you will choke off part of the air supply.

While I like the appearance and function of sheet metal duct there is a major cost difference between it and flex when done properly. In a attic space I would insulate both inside and outside of the duct and that gets very expensive. Items like duct wrap are available for the outside of the duct BUT it is a pain to install in a attic space.

Below are some rules for flex duct install according to SMACNA which is the true duct standard of install in the USA.