If you really want to...
Make a crosscut sled to make sure both are parallel with each other.
Have a look at anyone making one, note that you'd want a stable material for the runners.
Get some marker to colour in the surface of the edges, so the high spots will get the ink removed.
File and block for sure, could even be rebated to keep it 90 if you liked.
Seems like it would be easier to make a runner to suit instead.
Hope you have some suitable tools like a good engineers square at the very least, if ya don't, then wait till ya do before trying this.
Edit...And I should have added, having a known good straight edge/way of making one to a fine tolerance is a must.
A ruler won't cut the mustard here, as if you look at anyone making a sled, you will see how much the smallest error will jam the sled, so might be a good idea to make sure these are not only parallel in the first place,
but of consistent width, a calipers here, or a tight fitting block to check.
The use of a hand plane here if needing to make straight edge/block for checking width, or file holder, if you can't plane sharp edged flat blocks and lengths, then forget it, sanding blocks on say a belt sander likely won't be accurate to do this sorta thing.
Accurate planing ala David Charlesworth's methods will get you there.
You could devise a way of using one slot for running the file somehow on the other.
i.e don't do one until the other is finished.
Does this now seem easier to make a runner instead?