In addition to the individual circuit fuses, there are "reverse protection fuses" (Littlefuse type 257) in the converter panel, did you replace those? They are between the battery and the converter, so would explain why you work on Shore power and not on battery.
I wouldn't worry about the flickering until the battery is back in the circuit - it acts as a buffer for the converter.
If it's not the protection fuses in the converter panel, there's usually a breaker or fuse near the battery, and that could have blown.