If the Confederates built ironclads, they were playing to a strength of the US. The US had far more iron foundry and milling capacity. It had a world class steam engine industry centered on New York, Brooklyn, Newark and other nearby places like Patterson, NJ. The scale of the industry allowed the New York competitors to hire the best designers, industrial engineers and mechanics. Even the US navy had to compete with private industry for the skills necessary to compete.
No matter how inventive they were, and they were determined to do their best, they were going to get out built and out powered. Which is exactly what happened on the Mississippi River, and at Mobile Bay and finally at Fort Fisher.
The time and money could have been better spent on forts, mines, artillery and railroad maintenance.