Engine runs rough over 35000RPM - 1999 Volkswagen New Jetta

Jodesha, Should have scanned for diagnostic codes, have engine and transmission mounts checked. Check for vacuum leaks and or injectors could be a problem.
Check the attached links,instruction and guides on diagnosing rough running engine. Good luck
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How to Fix Rough Engine Idle Problems at YouFixCars com

https://www.2carpros.com/articles/engine-misfires-or-runs-rough

The Lost Art of Diagnosing Engine Problems

Rough Running Engines Car Repair Information From MasterTechMark

What are the trouble codes set? Get them read for free at most auto parts stores.

Change coils,fuel filter and check the code.

hi Jhlightcap.

The Common Problem: Rough Running Engine

A properly-operating engine should run smoothly and without excess noise. If your engine starts operating in a manner that gives you the perception of "running rough", it is likely due to a handful of common causes. A mechanic would investigate these common causes first in order to rule out a simple explanation for the engine's unsatisfactory operation.
The common causes for rough running in an engine are:

• Engine miss
• Vacuum leak
• Dirty fuel injectors
• Carburetor problems
• EGR valve
• Ignition coil
• Spark plug wires
• have a look at this link.

Rough Running Engine James on Engines 2

unplug ur main wires an make sure there dry

what are the codes

It can be issue with low fuel pressure,the fuel pump is getting old both needs to be checked.Also get the IAC valve checked.
Go through the related help links with similar problem,it may help:---
Click the links below:---
Engine Idles Rough and Dies? http://whatisbyme.blogspot.in/2012/05/1994-lexus-es300-engine-idles-rough-and.html

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van idles rough? http://howtobyme.blogspot.in/2012/01/2004-ford-freestar-van-idles-rough.html

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runs lean and idles rough? http://technoanswers.blogspot.in/2012/02/ford-runs-lean-and-idles-rough.html

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Car still runs Rough after tune up?

http://howtobyme.blogspot.com/2011/12/car-still-runs-rough-after-tune-up.html

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2006 kia rio runs rough http://technoanswers.blogspot.com/2012/10/2006-kia-rio-runs-rough.html

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Idle flair is noticed on car? Rough idle? car will not idle? Erratic idle speed? http://technoanswers.blogspot.in/2012/02/idle-flair-is-noticed-on-car-rough-idle.html

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Rough idle, staling and Erratic shifting? http://technoanswers.blogspot.in/2012/03/rough-idlestaling-and-erratic-shifting.html

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These details will help.
Thanks.

Sometimes a rough idle like that is a fuel filter. As you've already done the plugs and wires the fuel filter would be my next bet.

Here is a list of possible causes. You should not drive the vehicle if the check engine light is flashing all the time, you can cause even more damage. It could pay to have a professional find the real cause.

Spark plugs that are incorrect for the application, cracked, improperly gaped or worn can cause the engine to misfire or run rough at all times.
An IC module that failed to correctly control the ignition coil(s) will cause the engine to misfire or run rough at all times.
Poor connections, broken wiring or wiring that has shorts to ground can cause the engine to misfire or run rough at all times. NOTE: Check connectors that might be pulled apart as the engine flexes or wires that short to ground as they pass near brackets or shorts to ground on the exhaust manifold.
Fuel injector(s) that are shorted, plugged or partially restricted can cause the engine to misfire or run rough at all times.
An ignition coil(s) that has low output, corrosion on the coil tower(s), is carbon tracked or arcs to ground will cause the engine to misfire or run rough at all times.
A PCM that failed to properly control the injector or ignition timing will cause the engine to misfire or run rough at all times.

Check and see if the EGR valve is leaking, to check this spray water on it at idle, if the water steams off the valve is leaking and is the source of your problem, also are you sure you hooked the new DPFE sensor up right? re-check it..