Why do I believe that we should we become aware of our metaphysical assumptions?

From a strictly metaphysical perspective, I guess that the important thing is to recognize what we are assuming in an "it just is" way, and what is secondarily explained in terms of these assumptions. 
If this is achieved to some extent; I think we can then compare metaphysical "systems" or schemes, and then there is a basis for choosing between them. 
For instance, one person may regard an explanation of freedom/ free-will/ agency as vital to him; but another person may desire that everything he considers important must be as it is, with no contingency, and no possibility of things being otherwise. 
Such personal imperatives will influence the choice of metaphysical assumptions. Or perhaps, when a person becomes explicitly aware of his own current imperatives, he may come to disapprove of them, and may then reject them.   
Simply to clarify what one actually is assuming - in a clear and explicit way - is itself something very valuable -- maybe essential when it comes to really fundamental matters. 
Personally, I want my primary assumptions to be the kind of thing that is knowable intuitively, by personal revelation - and without having to depend on communications that may be unreliable, from secondary sources that may not be accurate or trustable. 
This has meant that - over time - it has been necessary to reduce the dependence of my core faith not only on church teachings, but also on scripture. I have come to regard both church teachings and scripture as (for what seem very obvious reasons) unsure and unreliable. 
I simply cannot stake everything on the accuracy of scriptural transmission and interpretation, or the integrity of any actual modern institution - whether or not it calls itself a church. 
To generalize, and for a Christian, this means (among other things) "knowing" both God the creator, and also (and more importantly) the person of Jesus Christ for oneself; know them "here and now" as it were - and as the root of everything else.

This is edited from a comment at Francis Berger's blog