oki well think of it as trying to figure out BSP by just looking at the format

trust me that is completely impossible without knowing how the engine is utilising the format.
even rebuilding the geometry you must understand the basic vertex position, rescaling and point translation - and notice how many compilers for this format don't veiw it properly without bugs ... not to mention you can't feasibly work directly within the format, because it a binary compilation rather than a raw format.
for the image wad you require the instruction RLE compression routine (and to a lesser extent the compiled TRx also requires these)
really it is not truely feasable to perfectly support a format without knowing how it is access'd atleast - if not the main data layout.
else it is all just a pure guess, perhaps educated - but it'd be bloody lucki if your guess was right.
Tsu'va Oni Ni Jyuuko Fiori Sei Tau!
One block follows the suit ... the whole suit of blocks is the path ... what have you found?