Spent an hour or so on it today, tapped out all of the threads for the turbo bolts and got a bit of swarf out of the offending hole, looks like I was right and something was in there; probably something from work while I was getting the studs out. I also ran a die down all the threads on the bolts so everything screws in easily now. Manifold and nuts are also back on but not tight, will sort that next time I go up there and get it all running again