My 05’ scion xa has always had a problem with vibration and some ribration sounds when stopped at a light or parked but both go away when i put the vehicle in neutral. It got so bad at one point the seats would shake, i took it to toyota and they replaced all the engine mounts. The vibration isn’t as bad but very noticeable. Could it be the A/C? The problem exists with or w/out the A/C on including thwe heat.
Since vibration occurs with the car in neutral, then it’s a simple matter to do some troubleshooting at home. With the hood open, just watch what happens to the engine during idle with and without the AC. Is it better when you rev the engine a bit?
He said the vibration STOPS when he puts the car in neutral.
What’s the engine idling at? It sounds like the engine is vibrating when under load. Since it’s always done this, it may be a characteristic of the car. But new plugs and filters can’t hurt.
As changing the mounts helped, I think the engine is mis-firing at idle for some reason or another and is shaking more than it should. It’s perfectly possible mis-firing symptoms would be more noticeable under load than in neutral. It’s hard to say why without more info. It could be a fuel/air mixture problem, or an ignition problem, or something more fundamental, like poor engine compression. Get any pending codes read would be the first step. And check for vacuum leaks, the hoses, the connections, and all the vacuum controlled devices.
One last thing. As said above, this could be normal to the car too. Maybe find another 05 Scion and compare it to yours.