Your overall plan of creating a slightly raised run to prevent mud and flood, with a sandy/gravelly fill, is certainly a good one to follow.
In a few details though you might want to consider some modifications. 1.5' high is really pretty tall -- not only is that going to require buying and moving Quite A Lot of fill, it is also (more importantly) a nontrivial engineering challenge to keep the sleeper walls from just busting apart under the pressure and weight of all that material wantin' to slump sideways. Even just a 6" wall will need tying down Really Well, although not nearly to the degree a taller one would. And honestly I do not think that there is any reason to raise the run more than 6" or so (ish) above surrounding soil level, unless the area is prone to deep flooding and if it IS then honestly you are in trouble no matter how ya slice it.
One thing to look into for aggregate to fill the raised run with would be "roadbase" or whatever it is locally called where you are (here it is apparently technically "A aggregate" <shrug>) -- it is generally about the cheapest aggregate that you can buy in bulk, a mixture of everything from dirt through sand through small gravel to large gravel. It drains good, is pretty easy on feet (unless maybe your local version has *sharp* rather than rounded gravel) and doesn't cost much. It's the stuff they use to make the foundation of roads, and to make dirt (gravel) roads/driveways.
If there aren't any aggregate co's in your area that will deliver a residential-sized load, then choose either sand, or sand and smallish not-sharp gravel.
Chickens can still scratch and dustbathe in any of this, no necessity for adding dirt. There won't be much in the way of bugs or plants growing in it, but there won't be much in the way of bugs or plants growing in a typical earthen chicken run *either*. Bugs will still wander in from adjacent lawn, and worms come up from underground; and you can toss safe-type plant material into the run for your chickens' enjoyment. If mud is a concern, I would recommend staying away from really fine small stuff, and removing it before it becomes too well incorporated itno the footing... but with a raised run, this will be less of an issue than if it were on grade.
One last small comment, maybe it's already the way you're planning it and I'm misunderstanding the phrasing but you will probably want to sink the posts for the run FIRST, *then* put in the retaining wall of landscaping timbers and the fill and the run wire and suchlike. And don't rely on the landscape timbers for preventing predators from digging in -- you will still need buried wire or (my preference) a horizontally-laid apron of wire.
With the good forethought and "preventive engineering" you're putting into this, I think you will be pretty pleased with the result and its ability to stay dry and as unsmelly and un-fly-y as possible
Good luck, have fun,
Pat