Kind of late answering but I do use a specialised mic which has a factory calibration file so that a flat response can be calculated. I use REW to make convolution filters that can be used by Roon or HQPlayer in my case. It's all small gains but I've stopped fiddling for the last 6 months or more so something must be working!!
When I had problems with high end harshness it turned out to be the gain staging between the power amps or digital speakers and the sources I was using. Make very sure that you are not sending too loud a signal to your power amps. It's worth knowing rather than guessing what the optimum headroom from your source to power amps is and even measuring the voltage of a reference level sine wave.
If you don't yet have a test disk I would recommend getting one, you can test your phono amp output to make sure you don't have a strong resonant peak in the upper frequencies. Certain cartridge/cable/phono amp combos will do that.
Sounds like you also have standard room mode issues in the low end. They are so predictable you only need to enter the room size into REW and it will accurately predict the frequencies.
I'm guessing the 48khz sampling rate is where the minidsp is economising.