Hi Jonas
I am surprised at your approach (seems complicated to me).
Here is what I do:
- select in mDecoderTool3 and its projects what is the one I like for the loco type (check by reference number which is closest to your project.
- check one by one all included sounds and replace them when appropriate
- program the mSD3 decoder (I use my CS3 or CS2)
- update the motor type (in the Märklin projects, often the motor types are not correct)
- prepare a loop of rails (R2 preferable) to allow the loco to do a self adjusment of parameter (writing CV7=77) and turning the speed knob and let go.

Cheers
Jean

Basically, I do the same as JohnjeanB

I start with a modern mSD3 project and change the motor type and only the following if needed:
Motor RPM Offset
Motor RPM Increase
Gear Ratio
Wheel Circumference [mm]
For the data on these above, I often use the data from older projects that used to be located under the m60_L55 folder. as these often have the data for older locomotives.
and note that there might also be errors in the old projects........ (and I probably have some decoders with incorrect data)

Then I do an automatic calibration, and if I remember correctly the Control Type is also changed during calibration if needed. (I usually start with Auto Pl controller)

I also do the chuff calibration manually and use the decoder values as a starting point only. But I'm no expert in this I just make it so it's fairly reasonable.
Note there was an article about chuff calibration in a "recent" Marklin magazine, but it was only very basic, without proper explanation.

As for sound, I do not use any old settings, in fact, I make sure that the sound configuration files are from a recent project with the latest options. As for the equaliser settings, those need to be adapted to each project in combination with the speaker used. but for standard Märklin speakers, the default settings are usually OK. (I still have i bit to learn here to get the best results)

I do wish that Marklin could have made a proper advanced manual for the mSD3/mLD3 with every setting in the mdecodertool properly explained.