05 Jetta 2.5 with odd headlight issue.
 

So about a year ago, the engine in my 05 Jetta blew up, so I went to a Salvage Yard and grabbed one, but they gave me a 2.5 Motor out of a 2010 Golf, so the wiring harness had to be switched out.

After getting it all back together, there was a loud humming in my right headlight and it periodically wouldn't function. When it didn't function, the wipers wouldn't function either, but when the headlight did function, the wipers did as well. We eventually found the issue to be a loose ground and tightened it.

Fast forward a month and my headlights started flickering, then the passenger side stopped functioning at all. Not only would the headlight not work, but the passenger side turn signal (both front and back) and tail light doesn't either. The left turn signal works, but when turn the high beams, they stop working. The high beam also switches back to low beam after 6 seconds.

We used a multimeter on the right headlight and on the lowbeam, it gets the 12V, but the highbeam only gets .4, even when switching from low to high and back. When checking the passenger side, it gets .2 pn one and .4 on the other.

I've been reading a lot of people have had issues with the switch, could this be the problem (and is there a way to test it?) or is there something more severe it could be?

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You need to get your motor scanned (preferably with VAG-COM\VCDS) for any error codes logged in the ecu and post them, that will save a lot of guessing and check systems out.