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Is it really necessary to have the trunk partition or divider for roof operation or not? I know that activates a switch but was wondering if the switch is not activated will the roof operate or not? My roof currently does not work and i’m missing the partition cover so idk if that is the problem i do get a message that says “close luggage compartment cover” or something like that, and thanks guys.
 

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Not having that luggage cover is at least partially why you are getting that error. The cover activates switches that allow the roof to operate. You could bypass the switches and get the top to work, but that brings about another issue. That cover limits how much can be put into the trunk and still operate the roof safely. Mess up the roof and you may as well trash the car. Replacement roof is around $15,000 to replace.
 
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Also when i open the trunk it does not swing up by itself, i have to manually pull it up all the way, does that mean the hydraulic pump is dead?
All sounds normal to me. The trunk should just make a small sound when you press the key fob, and then you open it manually.
The hydraulic pump is for the roof, not the trunk.
 

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The hydraulic pump is for the roof, not the trunk.
The hydraulic roof pump swings it out towards the rear during a roof operation, but plays no part in opening the trunk when the roof is fully closed or open. If you feel inside above the bottom edge they put two 'Hand holds' recessed in the back panel for pulling the trunk lid up and down. Mercs and other cars can have automatic trunk lid opening from inside the car. The EOS is manual.
 

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The hydraulic roof pump swings it out towards the rear during a roof operation, but plays no part in opening the trunk when the roof is fully closed or open. If you feel inside above the bottom edge they put two 'Hand holds' recessed in the back panel for pulling the trunk lid up and down. Mercs and other cars can have automatic trunk lid opening from inside the car. The EOS is manual.
Which is what I said.
Not sure why your directing this at me and not the OP
 

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It wasn't clear if the OP was lifting the trunk lid during a roof op or not and you said "The roof pump is for the roof, not the trunk", when it's opened and moved by the pump during a roof operation. An important part of trunk lid alignment when it enters the lock slot comes from hinges, pins and bushes in the hydraulic rams. Therefore it's relevant to know the roof hydraulics connected to the trunk lid may be part of the problem and shouldn't be ignored.
 

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The trunk will not fully open on its own. Once you lift the trunk lid a few inches, the struts should lift it the rest of the way. If they don't, replace them. They do wear out and are about $55 each from VW. Replace them both. Quick and easy job.
 

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I got them on eBay a few years ago for something like US $25 for the pair. Fit and work fine.
 
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