A. The official from X association
The person that I am talking about is coming from that association. I probably expect that person to act, while they are here, on behalf of that organisation.
B. The official for X association
That is one of our own people, not a member of, or acting for that association. It it the person, that for us, keeps in contact and deals with that association.
C. The official with X association
More or less the same as A), but in this case it is certainly true that the person is here in their role as member or representative of the association. You might hear this phrase on a news-item, if someone is called upon as an expert: "And to answer some questions about X, here is ms. Y, who is with the X association."
D. The official at X association
The person is working for, or physically at the premises of X association, but I am not necessarily talking to or otherwise communication with them.
"...substitute for the criminal justice system..." is correct in your example. You always substitute something for something else.
I can think of a situation in which you'd use "to" after "substitute":
I used a substitute to avoid going to the grocery store.
However, in that example you're just not saying the part where you've substituted something for something else, shortening the sentence. The "to" phrase isn't telling us what was substituted; it's just telling us why something was substituted. We can include it with the other part:
I used a substitute for the buttermilk to avoid going to the grocery store.
or
I used a substitute for the buttermilk in order to avoid going to the grocery store.
The "to" has nothing to do with "substitute", which pretty much always takes "for".
Best Answer
Since you mention "formal" you might prefer "With whom do you think I met?"
There is a small difference in meaning between "meet", and "meet with". The former suggests a short chance event. "I met John at the shops". The latter suggests a planned meeting. "I met with John to discuss our plans" This distinction is flexible and not always observed.
Hence use "Who do you think I met with" to ask "Who do you think I had a planned meeting with". And "Who do you think I met?" to ask "who do you think I bumped into"
In either case, asking such a question is very conversational, rather than formal.