The Morrill Tariff, which you misspelled, went into effect after Secession.
Thus, the Morrill Tariff had no legal impact on Charleston's failure to negotiate directly with foreign shippers and foreign businesses before Secession.
The Warehousing Act of 1846 applied equally to the Port of New York and the Port of Charleston.
Before Secession, there was no legal reason why a foreign ship could not sail into Charleston Harbor and deposit its cargo into a bonded warehouse in Charleston.
So, my original conclusion stands. If the Northern states and Lincoln had allowed the South to peacefully secede, business commerce between the North and South would have continued normally.
The reason Charleston did not negotiate shipping and trade agreements with foreign nations before Secession was because - economically - it made more sense to negotiate those agreements with the Northern shippers, Northern traders, Northern bankers, and the Northern textile industry.
Charleston had a non-slave population of 26,000 in 1860, and it was surrounded by rural farmland.
New York City had a non-slave population of 800,000, and was within one day of travel of another 1 million non-slave consumers.
Before Secession, it appears to me that Charleston made a completely rational, unforced, economic decision to do business with the great population centers of the North.
Why would that have changed after a peaceful Secession?
That was not an assertion of mine. You asked: "And why were tariffs different in different cities? Did some states and local ports charge additional tariffs? That was the reason for the difference.
Well yeah their was. It was 800 miles further South and did not have as good of port facilities as did New York.
Why would you add a couple of weeks to your trip just to land at lesser port facilities and a smaller potential market?
Sure they could do it, but why would anyone want to? The tariff's were the same. The market served was smaller (at the time) and so it just didn't make good economic sense or good labor sense to do so.