Sorry for the double post people, but I don't want to taint this post with the previous one.
Great news: I'm actually,
finally, able to play the game properly and make some progress!
I discovered that the intermittent game startup lockups were most likely caused by MSI Afterburner. It also locked up while I was moving around the map. It started working straight away after I stopped running Afterburner, however. Naturally, it carried on working when I restated Afterburner just to muddy the water.

However, I was running version 4.0.0 and there's a 4.1.0 which I installed and so far so good.
Yeah, the game saves really suck, but that's the way the game is designed unfortunately. Basically, it looks like if you die during a mission, you restart from the latest checkpoint, which is what you want. However, saving the game and going to the master menu forgets those checkpoints and drops you back to the start of the mission. Why the hell Ubisoft would do this I have no idea, but it's dumb and inconvenient. I'll look out for this "feature" when considering the next Ubisoft game and may well avoid it. Never mind, I paid a lot of money for it and the gameplay is good, so I'll persevere.
Finally, the PC still has its slight stability issues, especially when going into sleep mode, but there's no rush to fix this (I have better things to do) and doesn't impact the game. I'll start another thread about it if necessary as it's unrelated to FC4.