I used a dial caliper with a depth gauge but confirmed the piston heigth number with flat feeler gauges. The curve of the piston makes it difficult to measure.
If it matters, my engine is a K4 according to the numbers. My brother was thinking there were very slightly different cylinder block heigths from different years. Not sure where he got that info. He is usually right.
Starting in the K4 (until the K6), the "varying height" issue started with the cylinders. Honda added several heights, like 0.25mm, 0.4mm, 0.8mm, and [I have even seen] 1.00mm extra height to the cylinders. By the K5, the pistons appeared to have shorter crowns because they would often be sitting down inside the deck at TDC.
I think (IMO, here, based on conversations with Honda reps of the day) that Honda was cognizant of the hard-to-get gasolines in the US at the time, due to the gas shortage (from the Arab Oil Embargo we imposed). The ads were showing up to 50 MPG, running on Regular gas, instead of Premium. The least expensive Engineering change, on Honda's part, would have been to lower the compression by making taller cylinders, and this could have been easily accomplished by not milling off as much of the bottom and top of the block before installing the sleeves. At first, I surmised that they could "get" 0.25mm from the existing molds because they were likely milling about 0.5mm (total) to clean them up (top + bottom), and all they needed to make them even taller was some shims in the molds. If you look at lots of K4/5 cylinders, you'll often see little evidences of a shim at the base, in the form of a slight raised ridge at their seams. If you also measure lots and lots of cylinders, you will find quite a variance between them, although today it's hard to tell if someone may have beaten you to the punch before you milled it, with their mill job.
The guys who were building the turbo motors in the late 1970s and early 1980s coveted these taller cylinders, too, just to get the compression down to 8.8:1 with a +4mm cylinder and one extra base gasket, instead of a steel shim gasket and 2 base gaskets (a combination which tended to leak right near the cam chain tensioner, from the oil feed tunnels).
The K0-K3 engines generally had the stock height, which caused problems with Powroll pistons, as one example: these had taller shoulders that would hit the head. Many of these needed the shoulders turned back just to fit. IIRC, it was almost 0.8mm of too-much height in those parts. A copper head gasket appeared in 1974 (I've forgotten the vendor) that came in 2mm (0.080"), 1.75mm, 1.5mm, 1.25mm, and 1.00mm (0.040") thicknesses, and in the ads I remember, were shown sitting over Powroll's popup11:1 pistons in an open engine. It was advertised as the "turbo engine solution" head gasket (for those of you who might have old CYCLE or MOTORCYCLE magazines of the era?), in sidebar ads...
So, at worst case, maybe turning off the shoulders of the pistons would solve it handily? I wouldn't suggest deepening a quench band into the head, but that's another viable solution. Who knows, maybe you'll invent something new and cool!