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I've replaced a bad TB (TPS died).
Clean the area around the TB, top, sides, etc. debris = bad inside intake.
Basically remove the air box, remove the MAF tubing as a whole, TB can be Carb cleaned in place, just make sure that there is no debris that might get sent into the intake. The gasket goes for about $7. To remove the TB and clean it (IMO slight overkill), the electrical connector needs a small flathead screwdriver slid into the catch from the dashboard side of the connector. (towards the front of the car.) Allow lots of drying time 1 -2 hours to eveaporate excess spray fluid. Clean the MAF while your at it (carb cleaner is fine).
VAG-COM when reassembled.
 

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Re: (MastaVR6)

BTW I bypassed the coolant flow during the replacement.
For the electrical connector, small thin flathead in from the rear of the connector towards. if it doesn't name sense, have a
then look again, or have someone else look at it for asecond opinion. At first I thought mine had been glued in by the dealer, but my roommate pointed out that the wedge was apperently releasd from the backside of the connector.
It shouldn't be forced off, I don't think it would be cheap to replace the harness.
My notes:
I've got pics, I had to bypass the coolant flow through the TB. On GTI's (facing the front) coolant goes down in front top of TB and (elbows) out the right side front on the bottom. (see link below). The exit port (GTI) is the cavity just below the brass tube (lower left in pic). it is not tapped for the Jetta part.
A Jetta TB crosses the bottom front to back, exiting in the rear of the TB and out the bottom right side. in the pic the bottom-most hole is missing the brass fitting to connect the hoses too. Jettas have the runner tube going across the bottom.
see http://forums.vwvortex.com/zerothread?id=1021823
You will need an allen wrench to remove the 4 bolts holding the TB to the manifold, (mind the ground wire on the lower front bolt, at least mine had one). I would get the gasket too ($7 at the dealer). Be sure you can get the Throttle body "Adapted" (VAG-COM) when your done, your car will be happy you did. While disconnecting will clear CEL's, it won't retrain the TB to know what zero open is.
Clean around the TB area before starting- you want to avoid getting dirt inside. The clamps can be a PITA to remove. don't break them, be patient and walk them down the hoses to remove them. I used the existing hoses and rerouted them them to bypass the TB. no extra parts needed.
Pics for my TB swap here:
http://f1.pg.photos.yahoo.com/kmattwood
TB swap. shows the swapped parts, and old/new hose routing.
 

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Post your VAG-COM errors?
Does it run better after running the engine for about 20+ minutes?
When my TPS was failing, it was less likely to stall/run roughly when it had been driven 20+ minutes. IMO, that when the sensor warmed up via the heat rising from the headers resulting in better electrical contact.
 
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