Here's a quick update, I found one loose hose from the HVAC system on the engine compartment, at the moment I blocked it with a small screw and the van runs smoother and the shifting is back to normal so IN CONCLUSION A VACUUM LEAK WILL CAUSE SHIFTING PROBLEMS.
I will post back with any update about the P0401 DTC, hopefully it must have been the improperly fitted EGR valve green hose.
PS. I forgot to post this pic to show you how far will the shift lever will travel:
Any idea on how to fix that?
UPDATE:
I've found the tenth post within this thread describes how to re-align the TRS, I will give it a try and post back.
http://www.automotiveforums.com/vbulletin/t532817.html