2010 Prius, asks to put in Park, transmission shakes in neutral/park

Hello, so I got this problem out of nowhere. After work, I got into the car, started it up and it started shaking like crazy, it was coming from beneath the car (not the front, so probably not the engines fault). I shifted to drive and car asked to shift back to park and exclamation point came up so I didn't drive the car. Another day I drove it to my garage, again, it started shaking, but now not in park, but in neutral and in drive. When I was driving, shaking disappeared for ~ 1 minute, but then it came back up. About 1 year ago, something similar has happened, but I just shifted to drive and it disappeared. Any ideas what could be wrong with it? Thank You.

 

It sounds like two pieces knocking together, but when I disassambled gearbox, everything looked fine, my friend had another gearbox and flywheel, I installed that, but same problem exist. It has around 160k km.

 

I disassembled it now, when this happened, but everything looked good.

 

2 days ago my friend connected his computer to check the codes, but it showed nothing, so I did some research on my own (that's why I installed new gearbox and flywheel (my friend had it lying around so it cost nothing for me)), today we connected computer again and it showed that the engine or spark plugs are bad, as far as I know spark plugs were never changed in 160000km so I'm really confident that spark plug/plugs are causing this and when car asked me to put it in park I forgot that I need to close the door (STUPID ME). I'll give you an update on monday, I'll take a look at the engine.

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