If it's working, it's probably OK.
I suspect that the RD04 CDI is just two RD03 (or Transalp) CDI's in a bigger single resin filled box, but I'm fairly sure from vague memory that there are some additional connections between the two circuit boards inside the resin. If you had two wiring diagrams side by side you could probably work it out, but like I say, if it's working, it'll probably stay working.
Bob