I see there’s some things unplugged under the hood like this high idle sensor.
Since your switch doesn't work, this doesn't matter unless you want to go manual control.
Any reason why the RPMs seem to be very high once getting past 40mph? I can’t read them but the engine sounds like it’s working a lot harder than it needs to be. Albeit the IP is leaking as it runs and like I was saying before the diesel smell is strong while driving.
If there's any air getting into the fuel system as the engine runs, it will be hard to impossible to diagnose this. What you're probably hearing is air getting into the IP at certain throttle openings. This will cause the timing to go full advanced inside the IP and it will result in a loud, clattery noise, but not an increase in engine RPM.
The manual trans also makes some kinda noise until you push the clutch in and it goes away. Not sure what that is. Maybe a worn bearing or low fluid?
My first guess would be the input bearing inside the transmission. There's no way to know how long that bearing will last. It could be 100 miles or it could be 100,000 miles. It's not the throw out bearing like someone will probably suggest. Pushing in on the clutch pedal disconnects the transmission from the engine so the input shaft of the transmission will stop turning. The throw out bearing, on the other hand, will only turn when the clutch pedal is pushed in, assuming that everything's working right. I knew that four speed that came in my 1985 had input bearing issues. Not only could I hear a bearing noise while the clutch pedal was pushed in, I could also feel a vibration in the clutch pedal with it pushed in while the truck wasn't moving. It turned out that the sleeve that the throw out bearing rides on was actually broken off. Not a big deal since that bearing was making noise and there was extra bearing noise from the transmission while in gears 1-3. I only discovered the broken sleeve while I was swapping in the ZF5 that's in it now.