Hi goodwithtools,
I wonder if your speakers are not quite optimal for Atma MA-1s (even with your upgrades). According to Atkinson's review the Alexias are quite demanding. I changed from a Krell FPB600 to MA-1s and have not looked back. I followed Ralph Karsten's advice and bought speakers designed for OTL amps (Audiokines Dream Makers). The amp/speaker match is now excellent. After I got their effect speakers too, to fill out my rather large room, I sold the Velodyne DD18 sub, no need for it. Especially now, with the Aesthetix Io back from repair. It sounds amazing.