I made the tubes 24 inches long. Not sure how much is above the side of the bed. You could make them shorter or higher depending upon your application. I did not want to go too tall for when the tail gate is open, the sides are not as sturdy.
Don't forget to save the plastic inserts from the bed and re-locate them to the top end of your new tubes. They should fit over the outside and just make the install a little neater.
Your wood bedrail up by the cab will need to be placed inside the bed as the clearance to the cab will not allow them to be mounted on the outside like the side rails. Of course, you could mount the wood side rails on the inside of the bed all around. I did not , because I liked the look of them on the outside of the tubes on the sides.
I assembled everything and then took it all apart and painted several coats. Let dry and re-assembled.
If you have any other questions, please let me know. It is all pretty straight forward.