Those are interesting issues and you seem to have explained them quite well. I'm not a tech, just a DIY like most folks, but I'm not afraid to modify my car, which means I've had to learn a few things about it that I otherwise wouldn't have. Plus I've learned a lot from the folks on here, too.
The only Malibus I've actually owned and worked on are my 3 Gen7 models: 2009, 2011, and 2011. (Flood loss on the 1st 2011.
) That said, my ideas below are just that, ideas. I hope they help.
1. Since the actuators work when the gear selector tells them to then the locks themselves are not the issue. Based on the Gen7 schematics, both door lock switches are wired to the BCM (body control module) on individual terminals, then inside the BCM they are joined into one input to the computer itself. The BCM takes the input and sends the lock/unlock signal to the doors. Depending on trim level and/or personalization settings, the driver's door can be unlocked separately from the other three doors, such as when using a key fob.
It's very possible that it's both switches. There's actually a third switch that many overlook - the driver's outside door lock! See if using that makes the doors lock and unlock. If so, then you probably just need to take the two switches out of the doors and overhaul them. It takes attention to detail and some time, plus you have to be careful when disassembling them so that you don't drop something, and you want to observe how they're assembled so you can put them back together and have working switches. If that's not in your wheelhouse then you might try finding some in a junkyard.
1a. I'm not sure about programming key fobs. In some years, possibly yours, they can be programmed by using the ignition key and going through a series of quick steps. In other years it takes a trip to the dealership or someone with a Tech2 scanner. Search this site and/or wait for others to chime in with more info.
2. In Gen7 models, the intermittent position sends a reduced-voltage signal to the BCM on the exact same wire as Low and High. Additionally, High sends a signal to the High-Only wiper relay under the hood to provide full power to the wiper motor. If we exclude High, then on Int and Low the BCM receives the signal on the same wire. Low goes through one resistor and Int goes through as many as five additional resistors, which the BCM interprets as your choice of delay interval. So, if you can find the terminal on the BCM and carefully test it for voltage you should be able to determine if the voltages are getting there for Int or not. If they are and the wipers never pause then I'd say it's a BCM issue. If the voltages are not getting there then I'd say it could be the wiper switch/stalk itself.
3. It almost sounds like the clutch is slipping and can't keep up with engine speed. Once the engine slows it's able to regain some purchase on the compressor. The noise, though, is disconcerting. It could be the clutch or it could be an idler pulley. Or it could be something altogether different.
Those are my thoughts. I hope some of them help.