Regeneration and the Spirit

On the regeneration/filling question, they are different. The Holy Spirit has a multi-faceted ministry. When we are born again (regenerated), the Holy Spirit gives life to our spirits. At that same time he indwells us, mystically uniting us to Christ and remaining with us himself as the source of our life (this is his indwelling). Also at the same time, he gifts us in some way for ministry (1 Cor. 12) — is his this aspect of his ministry to which the Bible usually refers when it talks about "filling," as evident by the things people who are "filled" are said to do by virtue of this filling, such as prophesy and utilize other gifts (Luke 1:41,67; Acts 2:4; 4:8,31; 13:9; Eph. 5:18). But the gifts he gives us for ministry may vary throughout our lives. He gifts us as he sees fit for the purpose he has for us at a given time. So, whereas our regeneration is permanent and unchanging, as is the Holy Spirit's indwelling presence with us, filling is variable. Our gifting is related to the indwelling presence of the Spirit, but it is neither permanent nor unchanging (Rom. 11:29 refers to gifts to the entire covenant community, such as those mentioned in Rom. 9:1-6, not to specific manifestations of spiritual gifting in individuals).

John 3:3-5 is about regeneration, giving life to our dead spirits.

Luke 11:13 is not so explicit. Perhaps Jesus has in mind all of the different things that the Holy Spirit does. But from the context of exorcism "by the finger of God" (v. 20), my tendency with this verse is to emphasize spiritual gifting.

Acts 19:2 appears to be speaking about spiritual gifting. The people were faithful Jews as disciples of John the Baptist, but had not yet heard of Jesus (a situation which was possible only at that transitional point in redemptive history). Perhaps they were already saved, regenerated and indwelt by the Holy Spirit, but we cannot be sure. At any rate, they certainly had not been gifted. Paul rectified this after preaching the gospel to them. When he laid hands on them they received the Spirit's gifting, which the Spirit manifested in them via tongues and prophecy (v. 6).

1 Corinthians 2:12 speaks to the Holy Spirit's continuing indwelling presence and witness in the life of a believer. It speaks of the way the Holy Spirit gives us our faith and helps us understand spiritual matters on an individual level (as opposed to gifting which is for the benefit of the community; cf. 1 Cor. 12:7).

Ephesians 3:13-14 speaks primarily about the continuing indwelling presence of the Holy Spirit, as I read it. "After having believed" means that it is post-regeneration, and "who is given as a pledge" speaks to the possession of the Holy Spirit himself, not simply of gifting from the Holy Spirit. No doubt gifting is partly in view as a benefit of possessing the Spirit, but it is not the primary referent. Rather, it is the Spirit himself who is given as absolute surety to demonstrate that we will receive our full inheritance in the future.
When the Bible speaks of people being "filled" with the Spirit, it is generally talking about gifting (primarily in Luke-Acts, but also in Eph. 5:18). When it speaks of the Spirit dwelling in someone (e.g. Rom. 8:11), it generally refers to the mystically union between the Spirit and the believer, and the continuing presence of the Holy Spirit with the believer. When it speaks of regeneration, it usually uses fairly explicit language that lets us know it is speaking of that very specific work of the Spirit (e.g. John 3:3-8).
Sanctification has two different major definitions, and either begins at the moment we are regenerated or at an unrelated time, depending on which definition we intend. On the one hand, "sanctification" is a "setting aside as holy unto God." This is the primary meaning of most uses of "sanctification" in the Bible. Unbelievers can be sanctified in this manner, by virtue of their participation in the visible church, for example (e.g. 1 Cor. 7:14). Since unbelievers can be sanctified in this way, clearly this can take place without reference to regeneration, indwelling or infilling.

On the other hand, "sanctification" is often used as a technical term in theology for the process of maturation that a believer undergoes. In this sense, the term means "purification or cleansing." This process begins at the moment of salvation, simultaneous with the new birth, faith, and justification. I'm not aware of any instance in the Bible where the term is used exclusively with this meaning. It appears, rather, that the Biblical authors used the word to refer primarily to "setting aside," and sometimes included or implied this second meaning along with the primary meaning. The secondary meaning is more commonly included by Paul than by other New Testament writers, and seems even to be the primary meaning in a few instances (e.g. Eph. 5:26; 1 Thess. 4:4).