Vibration from trans?

I doubt it's in the trans or axle if it vibrates in neutral...

It's most likely in the rotating assembly...

The flex plate, torque converter, crankshaft, vibration damper...

The outer ring on the vibration damper may have slipped and is mis-clocked... The way to check/verify is to get a dead stop TDC tool and verify TDC by putting the engine at TDC and make sure the timing marks are correct...