So does that mean there would be 12" between the adjacent wall cabinets and the 36" high counters on either side? That's too low. Or just these three cabinets would be low?

What if you mounted everything at regular height (24" above the desk) and added an open shelf below?

I think 24" is ideal too. I can reach the bottom cabinet easily but don't have cabinets in my face while I'm working. 17" plus light rail will feel too low, IMO. For me that's head-bumping level. :-)

I don't want a narrower shelf below as I want all the paperwork clutter stored behind closed doors as this is a rather formal family room. The idea behind this system is to keep the clutter hidden and organized.
The tops of all counters, including those on the desk, will be 29.5" from the floor. I was proposing that the bottoms of all 3 cabinets above the desk begin 17" above the desk top. If that's too low, what do you think if I would make the three cabinets twenty inches above the desk top?

Oh I get it! I just sat at my kitchen counters and pulled my cabinet doors open 6" to mimic 12" deep cabinets over an 18" deep surface. My cabs have 18" of clearance to counter. I'm 5'6" and felt like I was in head bonking territory. I think with the cabinets that deep, I might want them at 21" or so.

Robotropolis, I'm unclear if you mean head bonking territory is when opening cabinet doors or also when leaning forward and looking down to do your paperwork so that your head is in danger of a good whack against the cabinet face frame? The bottom of my computer monitor is a little more than 7 3/4" above the desk surface and sits back about 7 1/2" from the front of the desk. I do paperwork constantly on the small desk area in front of the monitor and have never once come close to hitting my head on the monitor. If the problem is when opening the cabinet door, that can be done prior to sitting down. What is there about all of this I'm not getting?

Hi Texasgal, seems like you know what will work for you!

I am 5'6". When I sit at a desk, my head is about 24" above the desk. With cabinets set at 18" above the desk, 6" back from the front (12" deep cabinets over an 18" deep desk), the cabinets would be pretty "in my face" and I would risk bashing my head against the cabinets if I ever leaned over the desk. But it sounds like your planned use of the desk will not include leaning.

I've included a photo below (each square represents 3").

Wow, great illustration robo, thanks. That illustration and our back and forth has convinced me that I need to do a real life mock up with an open cardboard box set up on some book stacks on my dining room table to make the decision in vivo. I'm 5'5", and my table is 29.5" high so close to KM with counters. My plans are to have the paperwork piles and cabinet organizer inside the wall cabinets, on the lowest shelf. I want to see inside those cabinets to select and reach the right stack of papers. After experimenting with my natural style at the table, it appears that I lean back in a comfy chair about 7" from the table edge when writing, then lean forward at the table when searching for a paper. I may very well move the cabinets back down so that the light rail is 18" above the countertop, but need to experiement with the mockup. The 18" height would probably make many feel clautrophobic but everyone has their own style. You've been a big help in bringing me home to the reality that the 6" or so of counter before the wall cabinets begin is really very little distance.

I've given this more thought and have come up with a different approach but wonder if it will look stupid. What if the wall cabinets above the desk were raised so that the wall cabinet bottoms are 24" above the countertop as recommended. I've discovered that a steel 3 level horizontal letter sorter should easily fit inside a KM single door cabinet box that is 15"w x 12"h x 12"d. I would have it set on the desk top, pushed all the way into the furtherest corner where the two desk walls meet, with the cabinet back flat against the 42" wide wall section on the left side of the desk. Sitting at the desk area on the left, you would have 27"w along that back wall before enountering that cab box on the counter. Sitting on the right side of the desk, there would be a full 30" width along the back wall. A light rail added to the bottom of the upper cabinets would leave about 10.5" height left between the two. I' m getting inset doors, so a small knob could be put in the inset area so that clearance would not have to allow for protrusion of the knob when the door is open. Some type of decorative item could be set on top of the box for display. The counters will probably be finished the same as the cabinets so the box should not appear too prominent. I would like to have light under all of the wall cabinets above the desk. I can trust the GW feedback to be honest so please let me know what you think.