Peter (Iron_Dreamer) and I did a nice side by side shoot out between these two.
I honestly thought it would take a long time and scrutinizing to declare a winner. But the HE-1000 hands down wins in just about every category, Detail, Imaging, Texture, Soundstage, Frequency Respose, Phasing, Transparency, and Comfort. Maybe the SR-009 would win on Build Quality if it wasn't for it's shitty plastic headband and sling attachment that breaks easily. HiFiMan is not exactly known for stellar QC either, so it remains to be seen how well the HE-1000 holds up, but the build quality so far is a huuuuuuge improvement over it's predecessors. Notably the headphone cable connector is no longer that ultra crappy micro coax, it's now a 2.5mm mini plug on each side.
Transparency is probably the #1 crazy huge difference with the HE-1000. I thought the SR-009 was amazing with transparency, but the HE-1000 is just on another level. With the SR-009, when music is playing, you can still "feel" the sound emanating from the sides of your ears. Best way to describe in an exaggerated manner, is if you were to listen to music, and then put flat palms of your hands near the sides of your ears. With the HE-1000, that effect is nearly completely gone.
Major gripe is the headband size. In the beta test model, it's way too big. I have a huge noggin, and I have it one click away from it's smallest adjustment. That one definitely needs to be addressed, as I'm sure it will.
The EF-1000 amp is kind of meh for me though. It's way overkill, suffered from hums and ground loop buzzing too easily. And runs extremely hot. I know it's supposed to be a speaker amp too, but I'd just want a dedicated headphone amp. I don't run a speaker rig and headphone rig together.
The EF-6 Amp is perfectly fine. Even better if someone like Justin at HeadAmp made a high end UberAmp designed specifically for Magneplanar Ortho headphones like this one.