According to the product description the Kodiak stalls at 47 kts with full flaps, so 45 kts approach speed is probably impossible. I only had one landing with it so far, and I had no real problems controlling it with around 75-80 kts of approach speed. It really doesn’t matter unless you land at a truly short runway. I would definitely recommend keeping a higher speed on approach.
The autopilot issue you mentioned is interesting, because the exact same thing happened to me, only in the Douglas DC-3. The problematic altitude was also 2,000 ft for me, the AP went way under it, and tried to save itself from around 1,000 ft, at which point I had to intervene. I’m not sure which aircraft uses what kind of AP system but it feels like something’s going on in the sim since the latest update.