I just use
Speed Bleeders, makes one-man bleed pretty easy. That and a small bottle with a little plastic hose on it (that you see at every auto parts store). Various notes on the above:
1) Don't drain the system dry, always just flush new fluid in on top of the old. If you're worried about whether you got all the old stuff out, switch colors (ATE gold/blue) when you're doing a complete flush.
2) The manual says to disconnect the battery when bleeding. It doesn't make a lot of sense to me that this would make a diff, but I do it anyways, in case it keeps some part of the ABS from acting up somehow.
3) The bleed order in this car is right rear, left front, left rear, right front. I know it seems "wrong", but the manual probably lists it in that order for a reason (again, probably to do with ABS crap and/or how the pipes come together and their relative lengths).
Given where you're at, you're just going to have to work the system to get fluid back into everywhere it needs to be. Make sure it's filled and you've bled the obvious air out of the calipers. Turn the car on, and sit there in place pumping the pedal until either (a) it finally gets firm or (b) the fluid level gets low in the MC and you refill it and keep going. You might want to bleed the calipers again just in case once you get the pedal resisting a bit.
Then even after it seems bled and firm enough to be safe to drive on, you'll need to do some test driving and engage the ABS several times (as in, slam on the brakes and let it pulse) to spin up various passages it uses and get them filled (and the driving will help knock trapped air from the nooks in the calipers too). Then try topping off the MC and doing a little more bleeding. Eventually the system will get back to normal
.
When I've taken lines off (or calipers), I usually just put a ziplock bag hanging over the loose line while I work. You'll get some gravity bleed into the bag and a little air in the system, but it's just a few ounces. Just keep the MC topped up if you take a long time while the hose is hanging there in the bag.