Thought I'd post this for whoever is interested.
I did a hex comparison between my 3in1 and Wifi dumps and noticed that the junk data is written on a consistent basis. It seems that within the 3in1 save, at every 16KB, the junk data is written to the file. The starting point for where the junk data was written in my save was at 0x2000. Based on the established pattern of every 16KB, the next instance of junk data will occur at 0x6000, then 0xA000, 0xE000, 0x12000, etc., all the way until near the end, at 0x7E000.
The size of the junk data is also consistent as well. At the first instance (0x2000), the junk data ends at 0x3FFF. The difference between these two produces 0x1FFF, or 8191 bytes. This value remains constant for each instance of junk data. So, at 0x6000, the junk data ends at 0x7FFF, at 0xA000, it's 0xBFFF, at 0x12000, it's 0x13FFF.
That's it with my observations. I hope someone will find this useful.