I managed to get it out and welded a plug into the up pipe at the EGR cooler connection . sadly I didn't read your reply until afterwards. I agree, it is such a pain to work around the turbo that it would save time and frustration to remove it. I am going to work on putting it all back together tomorrow.
My up pipe clearly won't send anything into the EGR system so I was thinking it wouldn't matter how well the cooler sealed against the up pipe. Is it possible for boost to escape via the up pipe EGR cooler connection? I am a little concerned about that area as my weld is going to prevent it from sealing perfectly.