Francillon (page 61) indicates experimental & training machines were painted in 'bright training orange'. He has some monochrome diagrams (pages 73-74, 84) with the engine cowling painted a contrast colour, described as matte black in his two examples. Most cowlings, where different coloured, were matte black in his examples, but he describes at least one floatplane unit with a dark green cowling. The chutai designators (cobalt blue, red, white, etc) were usually applied as tail bands, not cowling colours.
Francillon also mentions (page 64) that later when the home islands were under attack, a green coat was applied on the top/sides, the bottom was initially left orange, but by late war the JNAF trainers were dark green top side, and light grey/natural metal underside.
A quick google led to a Japanese modeller's site
HERE
See
Appendix A: COLOR OF ZERO TRAINERS
It contains an anecdote about the green being applied over the orange on Kyushu.
Hope that assists.
