I haven’t had a 1.6 like yours, can you deal with the egr first? I think you have to tackle the broken stud/bolt. It will never seal otherwise.
If you have a picture it will be easier to understand what snapped and where, might be able to suggest a proper fix, I’ve had plenty to deal with over the years.
If you can do that in isolation and it fixes it then you won’t have to take the throttle body off again and have it aligned again.
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