I'll have to edit the "how to" to indicate the issue with dropping the pan. When you don't drop the pan there is still some fluid available for the transmission to pressurize the system allowing you to run through the gears, otherwise it's just sucking air. Do as Bart says and once the pan is back on with a bit of fluid in it then you can continue. It's not absolutely critical to get every last ounce out of the system, especially if you're using Mobil-1.
As for the bolts, I believe those are "security plugs" that some places like Jiffy Lube use to keep you coming back and/or prevent you from doing it yourself. A local mechanic friend was cursing up a storm one day when I stopped to visit and he couldn't find the specific tool for these plugs as he had one on the lift. Apparently they're not terribly common as people like my mechanic friend tend to beat the crap out of the installers when they can find them!Take a picture to your local NAPA and they should have a tool on the wall to fit.