From the numbers you have, on assembled bearings, it appears you're in the ballpark.
Honda's clearance specs were .0008" to .0012" for new (.001" nominal), with a service limit at .0032". The bearing "clearance" from their stated charts is supposed to be based on "0", which corresponds to the nominal 0.001" clearance. If you have, for example, a .0022" physical clearance in the journal-bearing assembly, then according to Honda's method you have a [.0022" - .001" = +.0012"] "extra" clearance, which is supposed to be "0" clearance. So, when you select a bearing from their charts, you're looking for a "0" leftover, which is an "invisible" .001". Which they accept as being .0008" to .0012".
After that's been digested.....
The "colors" of the bearing shells refer to the thickness of the shell material itself. Nominal is 1.5mm (0.05905"), but the length of the "crush zone" is varied slightly in manufacture, to make the seated bearing come out pretty close to [the ID desired + .001"], if at least close to round....
One of the things that's neglected in Honda's manuals (and I only gleaned it from a Yosh rep) was the .01mm extra case-to-case clearance "spec" for the Hondabond-like goo between the cases. What he told me, in 1973, was that Honda used 0.01mm shims between the cases to represent this clearance, then bored the cases. (This came up when my friend Jim "Chambo" Chamberlain align-bored his 130,000 mile K0 cases for his first rebuild...).
If you add the "missing" .01mm (.0004") to your case bore dimensions, things look just about right :(1.4171 + .0004) = 1.4175, for example. So, if you take:
1.4175" - (.05905" * 2) = 1.2994", and, in this instance, deduct the .0004" for goo you didn't have when you measured the cases, becomes 1.2990", just like the journals. That's the "0" number, which is supposed to leave you with "standard" clearance of .001".
The BLACK bearings will take you down .0004" on the ID size, from your present clearances, it appears. If I were doing it (like I'm about to do to my 750, next time it's apart), I'd use the BLACK at your #1 and #5, and leave the rest at the BROWN where you have them. And, break the engine in under 5000 RPM for the first 1000 miles. The outer 2 bearings on all of these engines suffer the most from torsional harmonics, making their bearings wear more. On CB750, for some reason, rod #3 often follows the same wear pattern as the crank's ends, never figured out why.
I don't know if I've explained it very well, but this all has to do with Japanese manufacturing techniques. They all seem to accept the "tolerance" of their fitups, or processes, or whatever, as the "0" or "target" value. Then, they only speak in terms of controlling their "deviances", which are those numbers outside of the "normal" tolerances. It's a little different way of looking at the world, but once you get used to it, it's not so strange. Just don't rebuild an American engine with the Japanese tolerances....you might need some really good oil to make it turn, if you did....