Moving tracks up and down...?

But that is ridiculous. Moving tracks or layers is standard practice in so much other software.

I assume you're talking about software like After Effects or Photoshop, which contain "layers" and not "tracks" in the way that Premiere Pro, and any other editor for that matter, have them . Perhaps it's a semantic difference, but it's an important one: in Adobe software, a "layer" contains one and only one footage item or graphical element, whereas a "track" can contain one or more footage items or graphical elements. In After Effects, you HAVE to seperate footage items by both time (X-axis) and stacking order (Y-axis)--that's simply how it works. However, with Premiere, you only necessarily have to seperate footage items by time (X-axis)--if you can do everything on one track, so be it.

If you were able to drag tracks up and down in the stacking order (Y-axis), you may be able to achieve the layering effect you want at a certain point in time in your sequence, but you would also change the stacking order for the entire duration of the sequence. This may be what you want, or what you don't want, but I would submit that most people would never need this kind of functionality. How often does one need to completely rearrange the stacking order of an entire sequence? I know that I never need this; it's only small portions of time where I need to rearrange items on the Y-axis. I just think this capability would be so rarely needed that there is no point adding it; it could potentially cause more trouble than good.

I'm currently working on something that has (at its peak) five small windows with different clips with lots of edits running with their own effects. At times I've wanted to reprioritise a track (to put it above another) so just draggng a track up would have been a quick way of doing it.

You might consider nesting each track (or track segment) in its own sequence, so at least you're only dragging one element up and down, instead of multiple small clips. Just add one empty track to serve as a temporary landing zone, that you can move an individual nest into, and then continue to reshuffle until you get the order you want. I realize this isn't what you really want, but it's the best workaround I can think of.

How disappointing - and a shame the project is too long for AE!

Why is it too long for AE? After Effects has something like a 3 or 4-hour limit to a comp, which I imagine would be pretty difficult for most people to exceed. It would be a bit of a pain to manage, I suppose, but you could do it.

Alternately, if you've got the suite and therefore Dynamic Link, just select the clips in the section of timeline you're trying to work with, and select Replace with After Effects Composition. That chunk of timeline will be sent to AE and the clips will be stacked as individual layers in the same order they're in in the PPro sequence. From there, you can organize and reorganize things to your heart's content, and that will be reflected in your PPro sequence. You may want to consider creating nested sequences in PPro first, because those will be recreated in your AE comp as nested precomps. Might make layer management a bit more friendly.