I had to read a book for Junior AP History class called Why the South Lost the Civil War. It seems you are making many of the same points. Maybe it was Why the North Won the Civil War. ??? Whatever.
You've neglected a major factor of why the Union struggled so much at the onset. They were the invading army on unfamiliar and tough, often marshy landscape. They also had not developed immunity to local pestilence and germs. Thousands died of malaria and dysentery. They did not know how to live off the land like Confederates so they were dependent on supply lines that could be and were sabotaged. The local population often aided the war effort through espionage, spying, misinformation, misdirection, and sabotage. Scouts were incredibly easy to pick off through guerrilla tactics until they learned better.
The point is, invasion is hard, an uphill battle if you will, regardless of armament, size of army, etc. Eventually those things will win out and are certainly more relevant today (with the advent of antibiotics) but only after great cost.
Further, the Confederacy never really invaded the North, with the exception of the Battle of Antietam and the Battle of Sharpsburg, all major battles were fought on Confederate soil. Perhaps if they had, they might have won. Though, to be fair, Confederate soldiers were sloppy with their gear. The South is littered with cast off equipment. And, as you said, they lacked the industrial might of the North to replace lost or discarded items readily. No amount of military strategic can overcome that deficit. Confederates also erroneously thought the war would be over in a matter of weeks.