Hello Lubliner,
You have posed an interesting question that I'll try to answer but first there are some details to clarify. The Louisiana and Mississippi were not sister ships. As you've noted they were entirely different in concept, design and construction. The Mississippi was larger and built as a CSN Department project with the Tifts acting as agents of the department. Their expenses were covered but they were otherwise uncompensated. They served out of patriotism toward their new nation. The Louisiana was built by a private contractor, Murray, who was given both incentives and penalties for finishing by a certain date. It was expected that he would make a modest profit from the construction.
The Mississippi was contracted on 5 September 1861 with her keel laid on 14 October. She would be launched only on 19 April 1862 and was set afire and scuttled off New Orleans on 25 April 1862. Construction was advanced enough for launching as early as late February 1862 but she was held on the stocks waiting for the machinery to be fitted. The Louisiana was contracted on 18 September 1861 with her keel laid on 15 October. She would be launched to much fanfare on 6 February 1862 and declared commissioned and operational on 24 April 1862 after Farragut passed her and the forts earlier that morning. She too would be set afire and scuttled off the forts on 28 April 1862.
Examining the various known contracts with the actual construction dates of CSN vessels, I have yet to find a single vessel built in the contracted period. This despite the bonus incentives or penalties included in the contracts. Consider:
Ord/Cont Keel Launch Commission
Carondelet 10 Jul 14 Sept 25 Jan 16 March
Bienville 14 Sept Oct 18 Jan 4 April
Morgan 10 Jul 1 Oct 31 Jan 25 March
Gaines Sept 2 Oct 13 Feb 25 March
Mississippi 5 Sept 14 Oct 19 April -
Louisiana 18 Sept 15 Oct 6 Feb 24 April
Those were all new construction projects started in 1861 under ideal conditions. These contracts were issued with the idea that construction would proceed as it would in peacetime, albeit in a faster fashion. They did not take into account the emerging lack of supplies, the confiscation of building materials, the conscription of mechanics and carpenters, the inflationary effect of a wartime economy, and actual attacks by enemy forces. All of these factors contributed to building delays. They did not allow the builders to collect any bonuses, nor did they allow the CS government to enforce the penalty clauses of the contracts. In worse case scenarios, the CSN would lose confidence in a contractor and simply seize the vessel and attempt to complete her by themselves (e.g., Arkansas). This still did not prevent the contractor, in this case Shirley, from obtaining further contracts later.
Most CSN contracts were structured so that a builder would be paid a certain amount based upon building progress. If a builder requested a contracted payment he would have to have a CSN officer inspect the vessel and sign off on the construction before payment would be authorized. For example, Hughes was scheduled to receive his 4th and 5th payments ($10,000 each) on the gunboat Bienville on 9 and 23 November 1861. Both payments were not authorized and released until 21 December 1861. I have not yet encountered a builder paying a penalty for delayed construction, but there is documentation of builders seeking payment for work done that was never compensated. That is especially true regarding the conversion of RDF gunboats.
All the best,
Bil