Sorted it now. Here's what I did:
1) rub the mold off with a moist cloth and leave the boots to air outside
2) rub a mix of white vinegar and water (dilute) onto the area affected, and then leave to air again
3) I then bought a toothbrush, dipped it in the vinegar and water mixture, and went around the gap between the side of the boot and the insole, then let it air out and dry
4) I bought an anti fungal/bacterial shoe spray, used that twice a day for one day, and gave it a few days to dry
5) rubbed tea tree oil directly on the sole and in the nooks and crannies
I now use the shoe spray every time i wear it. The first time i put the boot on again I recognised there was some white stuff in the space where my foot wasn't, turns out it was just salt from the sweat which couldn't escape through the leather due to the waterproofing i'd (stupidly) put in.
Hope this helps anyone with the same problem, although it seems like i'm a bit of an anomaly. Going to buy another pair of boots soon, start the rotation going!