R.T. Beckwith provides a good summary of the some of the changes that took place from the First Temple to the Second Temple in terms of physical objects within the sanctuary:
The information which we are given about the Second Temple is not sufficient to enable us to compare it in detail with Solomon's Temple, though a comparison of Ezra 6:3 with 1 Kings 6:2 indicates that it was twice as high, and other differences will appear later. At the same time, it did not have the idealistic dimensions of Ezekiel's Temple, nor did it have the magnificence of Solomon's Temple, to judge from the reactions it inspired (Ezra 3:12-13; Hag. 2:3; Zech. 4:10; cf. Tobit 14:5). The apparent inferiority was not simply one of adornment, for, as the rabbis were afterwards to point out: 'The Second Temple lacked five things which the First Temple possessed, namely, the fire, the ark, the Urim and Thummim, the oil of anointing and the Holy Spirit [of prophecy].'
The 'fire' is the supernatural altar-fire, which fell from heaven (2 Chr. 7:1-3). In the version of the saying given by the Babylonian Talmud, the 'oil of anointing' is replaced by the 'Shekinah' (literally 'dwelling'), which means the visible manifestation of God's presence in Solomon's Temple by way of the glorious cloud (1 Kgs. 8:10-11; 2 Chr. 5:13-14; 7:1-3). The loss of the ark at the Babylonian exile was a calamity which the people naturally felt with especial acuteness, and many legends gathered round its fate (2 Macc. 2:4-8; 2 Baruch 6:3-9). Josephus states in so many words that the holy of holies was now empty (War V:219). So the Second Temple contained none of the visible tokens of God's presence that there were in Solomon's Temple: his presence was now purely a matter of faith.1___________________________
1 R.T. Beckwith, "The Temple Restored," Heaven on Earth: The Temple in Biblical Theology, Eds. T. Desmond Alexander and Simon Gathercole (Carlisle, UK: Paternoster, 2004), 72-73