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Problem has been solved.
If anyone else ever has the same problem, this is what happened.
When the drop boxes go in, the transmission bracket is lowered 6mm.
The air filter box is only a couple of mm from the firewall, so when the motor tilted a couple of mm, the air filter box was sitting against the firewall.
And that's where the vibration came from.
The reason it stopped when I pushed in the brake or clutch, I was on an ever so slight hill, so when I pulled the handbrake on, it was enough to shift the air filter box off the firewall. So it wasn't the clutch or brake at all.