Dunno what to say in particular, because i have not used melzi and neither of the firmwares. But generally speaking, there are just a few files to look for. The normal config settings are usually in files like config.h and/or similar. The thermistor tables also have similar name. The uC pinout for the hardware chosen can be found in a file usually like pins.h. Normally i think these are all the files that would need some attention and there isnt any other config to do besides these. If you nail these down, you are covered. If the board appears to misbehave or some functions appear to be missing for example it could easily be so because of wrong pins definitions in pins.h.
What i meant about calibrating thermistor and extruder is rather hardware wise and generic. For example to find extruder steps/mm you make marks on filaments and extrude distance like 10cm back and forth, and check if the distance extruder corresponds to the distance ordered, slowly correcting etc till its exact match. This because can not determine extruder steps/mm mathematically because of squishing and hobbed bolts are not consistent, so it needs to be tweaked/calibrated. The termistor tables can also be calibrated with a thermocouple to make the temperature reported exactly match the temperature of the thermocouple. Its better to have it like that, but afaik not many ppls bother with it. If you do get these things from the original supplier it would save some effort of doing them again.
What i meant about calibrating thermistor and extruder is rather hardware wise and generic. For example to find extruder steps/mm you make marks on filaments and extrude distance like 10cm back and forth, and check if the distance extruder corresponds to the distance ordered, slowly correcting etc till its exact match. This because can not determine extruder steps/mm mathematically because of squishing and hobbed bolts are not consistent, so it needs to be tweaked/calibrated. The termistor tables can also be calibrated with a thermocouple to make the temperature reported exactly match the temperature of the thermocouple. Its better to have it like that, but afaik not many ppls bother with it. If you do get these things from the original supplier it would save some effort of doing them again.