All believers are indewlt by the Holy Spirit, even when they are out of fellowship. God still created humans as creatures with volition, meaning we are able by our free will, rebel from Him. We do not have the power to remove Him from us as once we are saved with eternal life, we are part of His royal family forever. So I suspect the Spirit of Truth resides in most Catholics, although many, just like other denominations, might not be in fellowship with Him.
Similarily with Catholic believers and the body of all believers as a whole, while we follow His enabling work in us with our volition, we may remain in fellowship with Him. This is also sometimes referred to as being filled with the Spirit, but is different than the indwelling of the Spirit, which is also different than enduement of the Spirit.
In regards to the passages presented, they don't seem to reflect the intent of the poster's argument.
John 14:11-12 reads of the relationship of Father and Son, and the significance of works performed through Him.
John 16:13 reads as though addressed to either the apostles or individual believers, those who believe in Him, although I do not have a translation which uses the word "Church", but instead uses the word, "you" in addressing to whom the Spirit of Truth will perform His ministry. (The New American Bible produced by the National Conference of Catholic Bishops and the United States Catholic Conference uses the word, "you" where the post uses the word "Church".)
1 Timothy 3:15 refers to Timothy speaking to his audience as to why he is writing, that if he should tarry long, they might know how to behave themselves in the house of God.
BTW, some advanced doctrine might be present in these passages relating more to how God indwells each and every believer, which Person of the Godhead is active, then how we work together amongst ourselves, through faith in Christ, with the unique gifts each of us has from the Holy Spirit. Perception of the passages from the perspective of a comparative religion, where a particular denomination owns property they drive to, walk inside and perform various religious activity is a different meaning of 'church'.
FWIW, I encourage all in these threads to read, think, understand, and memorize the meaning of Romans 10:6-7, but only after a simple thinking of God and quick confession of any known or unknown sin, and allow Him to write His meaning in our mind, then our hearts, so that while we remain in fellowship with Him, we might better perform through faith in Him in all things.
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