Thanks for the nice words :-).
... It it also my impression that MSB-first seems a popular representation.
well, anyone can parametrize how he or she wants... IrScrutinizer contains one protocol called "NEC-Shirrif" where the payload is one parameter ("data") in MSB-first format, for compatibility with the Arduino IRremote by Ken Shirriff (the current version is different though).
By the way, I noticed that the older irMaster has additional export options for converting pronto codes to wav files under "Output HW" for Audio such as "Divide Carrier" and wave form modulation. Have these features been omitted in IrScrutinizer?
You are right, some not very useful (and hard to explain) options have been removed. Do you miss anything in particular?