I got bored last night and so had a quick go at implementing a barebones blind stacking process that was totally self contained and and didnt use GPUs (not an area of programming I have ever had cause to venture into). To keep it simple I used Python3. It was able to stack a 60x 1Mpixel image set on a given drift/rotation rate in about 5-6seconds. So if you are wanting thousands of them, be prepared to wait thousands of seconds.
If you’ve a spare desktop knocking about then you can just start it running and come back in a few hours. Not a big deal.
Tycho wins though on being: 1, fast 2, fully integrated 3, largely already debugged and tested.
I think Python is part of the Linux install these days isnt it, so you can have some fun.