I know that this is a couple of years old, but I am having a similar issue. My glitch involves Hanharr. Just as the O.P., after having my PC go through the tunnels, get to the security door, play the cut scene that has you now taking control of Hanharr as your temporary PC, the scene fades and Hanharr is now outside the security door where the main PC should be with no way to continue. I tried reloading saves from before Jek Jek Tar with no success. I've even started new games; all with the same result.
I have a soft-modded Xbox (Evox) and I have a custom game disc (made an override folder and placed it on the disc using Qwix). I altered a few files: appearance.2da, feats.2da, classes.2da, featgain.2da, heads.2da, portraits.2da, spells.2da as well as the .uti files for all of the partymembers (I gave them better starting stats and skills).