hawk 37,
No, not really wondering why you're trying to re-create the wheel, it sounds as though you have an octagonal wheel and trying to convert it back to a round one !
There are a great many areas where the software creators for simulators use generally correct, generic, and simplified algorythms for simulators. Don't forget that the primary function of a simulator is to reasonably reproduce control characteristics for pilot handling qualities, often at the expense of loss of performance fidelity.
As an example, you quoted that you've tweaked your simulator for realistic best rate of climb, but the "speeds are substantially less than the flight manual in mach and cas". This one is familiar, the original programmer has done it perfectly for EAS (which we all would really like to have), but not accounted for compressibility which directly affests the CAS and Mach No., both of which you've found to be in error (in line with what you would expect if EAS were presented for CAS).
I'm no fortune teller, but can reliably predict that your prediction of correctly adjusting e / Cdo etc to fit one operational situation will affect other areas.
Lots of luck, find the happy medium.
Regards,
Smokey