Me, I agree with you that one has to try to work out what the Bible is saying, and let it say that even if what it says is uncongenial to one's personal prejudices or preferences. However, there are two possible reasons for doing that:
1. Because one thinks the biblical text embodies an authoritative utterance by a deity, which must therefore be accurately deciphered before one can decide how to act in accordance with that utterance.
2. Because one believes that the biblical text is an important piece of writing that can reveal interesting things about an ancient culture that has played a great role in the formation of the rich tissue of human culture, and one wants to find out what the ancient writer was really saying
I am basically (2); I don't pretend to read your mind, but I suspect you are basically (1).
Now as to the business of 'taking the Bible as a whole':
(3) If one believes that the whole of the present biblical text is composed of divine utterance (let's agree for the moment not to go into problems of different versions of what is to be called 'the Bible'), and if one believes that the deity in question is consistent through time, then it follows that:
(4) One is obliged to assume that somehow it is possible to make consistent sense of the whole biblical text taken together, and that no part is to be understood as contradicting or being inconsistent with another part.
Since I don't believe (3), I am not obliged to follow (4). Just to be clear, I don't believe there are any deities, and so I don't believe that any text contains divine utterances. I therefore see the biblical text as a tissue of human writings, edited by human editors for reasons that were wholly of their time and place - which is why (in the view of people like me) one seems to find different and sometimes not wholly consistent accounts of the same events woven together or repeated in different places.
As you will be aware, there are theists who see the biblical text as a human response to an encounter with their divinity, not as simple divine utterance. That leaves room for them to dissent from (4), much as I do. I gather however that you are not that kind of theist. That's fine by me. but I hope you will manage to find the charity and humility to concede that those who differ from you may be (in your view) mistaken, but are still neither dishonest nor stupid.
To go back to your point about the Psalms having a reference to mountains being thrust up at the time of the Flood, and therefore providing a refuge of plants (and presumably insects and other animals): I think you are referring to Psalm 104 'in the order of the Hebrews', in particular verse 8.
The key question here is whether what goes up and down is the mountains and valleys, or the water that flows into the mountains and valleys. Here are two early English translations which differ in that respect, with one version of each verse following the other (note that the Douay-Rheims version - what some people think of as 'the Catholic Bible' - has a different Psalm numbering). As you can see, the KJV makes the up and down refer to the waters, whereas Douay-Rheims makes it refer to the mountains themselves:
Douay-Rheims (RHE)
King James Version (KJV)
1 (103-1) Bless the Lord, O my soul: O Lord my God, thou art exceedingly great. Thou hast put on praise and beauty:
1 Bless the LORD, O my soul. O LORD my God, thou art very great ; thou art clothed with honour and majesty.
2 (103-2) And art clothed with light as with a garment. Who stretchest out the heaven like a pavilion:
2 Who coverest thyself with light as with a garment: who stretchest out the heavens like a curtain:
3 (103-3) Who coverest the higher rooms thereof with water. Who makest the clouds thy chariot: who walkest upon the wings of the winds.
3 Who layeth the beams of his chambers in the waters: who maketh the clouds his chariot: who walketh upon the wings of the wind:
4 (103-4) Who makest thy angels spirits: and thy ministers a burning fire.
4 Who maketh his angels spirits; his ministers a flaming fire:
5 (103-5) Who hast founded the earth upon its own bases: it shall not be moved for ever and ever.
5 Who laid the foundations of the earth, that it should not be removed for ever .
6 (103-6) The deep like a garment is its clothing: above the mountains shall the waters stand.
6 Thou coveredst it with the deep as with a garment: the waters stood above the mountains.
7 (103-7) At thy rebuke they shall flee: at the voice of thy thunder they shall fear.
7 At thy rebuke they fled ; at the voice of thy thunder they hasted away.
8 (103-8) The mountains ascend, and the plains descend into the place which thou hast founded for them.
8 They go up by the mountains; they go down by the valleys unto the place which thou hast founded for them.
9 (103-9) Thou hast set a bound which they shall not pass over; neither shall they return to cover the earth.
9 Thou hast set a bound that they may not pass over; that they turn not again to cover the earth.
From a source such as
THIS ONE, you can easily see that different translators still differ on this point:
New International Version (©1984)
they flowed over the mountains, they went down into the valleys, to the place you assigned for them.
New Living Translation (©2007)
Mountains rose and valleys sank to the levels you decreed.
English Standard Version (©2001)
The mountains rose, the valleys sank down to the place that you appointed for them.
New American Standard Bible (©1995)
The mountains rose; the valleys sank down To the place which You established for them.
GOD'S WORD® Translation (©1995)
The mountains rose and the valleys sank to the place you appointed for them.
King James Bible
They go up by the mountains; they go down by the valleys unto the place which thou hast founded for them.
American King James Version
They go up by the mountains; they go down by the valleys to the place which you have founded for them.
American Standard Version
(The mountains rose, the valleys sank down) Unto the place which thou hadst founded for them.
Bible in Basic English
The mountains came up and the valleys went down into the place which you had made ready for them.
Douay-Rheims Bible
The mountains ascend, and the plains descend into the place which thou hast founded for them.
Darby Bible Translation
The mountains rose, the valleys sank, unto the place which thou hadst founded for them; --
English Revised Version
They went up by the mountains, they went down by the valleys, unto the place which thou hadst founded for them.
Webster's Bible Translation
They go up by the mountains; they go down by the valleys to the place which thou hast founded for them.
World English Bible
The mountains rose, the valleys sank down, to the place which you had assigned to them.
Young's Literal Translation
They go up hills -- they go down valleys, Unto a place Thou hast founded for them.
The last translation in the list is one that tries to stick as closely as possible to the Hebrew:
iolu erim irdu bqouth al-mqum ze isdth
they-are-ascending mountains they-are-descending valleys to place-of this you-founded
I think you can see why two different kinds of translation suggest themselves here.
It may not interest you much, but some scholars see this Psalm as talking about the creation, when the primal waters were cleared from the earth. You won't accept this, since obviously there is a problem of consistency when v.9 (KJV) says:
9 Thou hast set a bound that they may not pass over; that they turn not again to cover the earth.
For you, I suppose that cannot be a pre-Flood reference on grounds of consistency. Others without that commitment may legitimately see things differently.