I have a 3? shim to accommodate the deep to medium height difference and plan on using blocks under the medium frames to minimize burr comb.
That is quite a clever idea for someone who is new to beekeeping ! Seeing as you are able to build your own equipment, another possibility (one I'm currently mulling over myself) is to make short frames - without top bar lugs - to be cable-tied underneath the mediums. Then the bees can build natural comb there to their heart's content. And then, whenever convenient, those short frames can be removed and tied together underneath a plain top bar, so that nothing is wasted.
Over here in England we have frames which are 6", 9" and 12" deep - so a handful of 3 inch 'short frames' would allow migration between the various sizes, albeit with a small amount of work involved. To be clear - I'm not suggesting that this ought to be part of a regular operation - just something useful to employ on the odd occasion, should a disparity of frame size present itself.