By the time you remove everything to get at it from the top... Upper plenum..etc etc .... you should just pull the transmission to access and remove the EGR. I completely removed my EGR valve with the engine out of my red TT during turbo replacement. But in any case there is this : https://conceptzperformance.com/wiki/index.php/EGR_Removal .........
"Bypassing Without Removal Due to tool, time, or physical restraints, it's sometimes impossible to remove the EGR system completely without removing the engine from the car. Many owners still opt to bypass the system, leaving much of it still in place but without function. After removing the plenum, install the plenum block plates on the underside of the plenum. See the "Bypass Kit Installation" section below. Using a cutting tool, cut the EGR tubes as far towards the back of the engine as possible. Be sure to have any pipes (turbo outlets, for example) completely covered to prevent metal shavings from entering Install a rubber cap (5/8"?) on what's left of the EGR tube. Use a zip-tie to secure it in place. If the EGR valve is functioning properly, it will actually prevent exhaust gas from flowing through these if it doesn't have a vacuum signal, but this is still good practice, just-in-case. Remove the EGR solenoid and associated vacuum lines. Check out the Vacuum Diagrams article for a little more help seeing how this is done."
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