Rebelstsea makes a good point. There was a pool of skilled shipwrights in the Confederacy. Fredrick Douglas worked as a caulker in a shipyard before he self liberated, for example.
The very able Robert Smalls is another example of the nautical talent pool that existed.
Link
www.nps.gov
The issue wasn't just a complete absence of organization at the top. Slaveholding was a profligate waste of human potential. Neither Douglas or Smalls would have been allowed to apply their natural gifts to managing a Confederate shipyard.
Wessyngton Plantation north of Nashville lost a succession of journeyman blacksmiths to good paying jobs in Pennsylvania. The skilled craftsmen that were absolutely critical for any coordinated creation of a flotilla of ironclads was were literally disappearing overnight. This was a double blow to Confederate hopes of independence.
The loss of a single journeyman, often including his family, was a minus one man day of skilled labor & a plus for the Union. That is a net two man days advantage times every self liberated craftsman.
Even had the Confederate government somehow imposed a strategic military plan coupled with a rational allocation of resources, the pool of skilled labor necessary to build the vessels was shrinking like an ice cube in July.
"Pook's Turtles" was the name given to the seven City Class ironclad gunboats built in 1861 were the work of Samuel Pook. The Mississippi Flotilla he created served ably through the brown water war. There is the blueprint for a Confederate ironclad flotilla right where it was really needed. Read more here.
Link
Civil War History and Stories
www.nellaware.com