I wouldn't let the MC drain completely. It'll just be a major hassle when it comes time for bleeding.
I wouldn't scoop the fluid out either, mainly because while you're swapping brake lines the fluid will be leaking out, and what's the point of leaking out brand new fluid if you don't have to? (if you let the level get down that far) Save the new fluid for the bleeding.
I would recommend having someone help you, mostly for their extra set of hands. If you can get someone to plug up the chasis hardline (where you attach the line) with their finger, you can slow the flow a lot, which should give you plenty of time to hit the calipers with some brake cleaner and reattach the lines. You can scrub the calipers once they're attached..
Just a sidenote, keep your stock bleeder valves around just in case. I bought a set of speed bleeders from SPL and for some reason I couldn't get two of them to work properly, so I had to put the stock bleeders back in and bleed it that way. Maybe it was something I did, maybe it wasn't, I'm not sure, but I'd keep the stock ones around just as a precaution.
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