Stevels,
Yes, you got it. To stop the engine, flip the stop lever UP and when the engine slows down a bit, flip the decompression cams under the exhaust lifters. In an emergency, you can also stuff a rag in the air intake.
Re: starting, it looks like you get it. You're trying to chase the air bubbles out of the fuel starting at the tank and proceding all the way to the injectors.
On starting, if you can get one cylinder firing consistentlly, it should be able to carry the other "dead" cylinder. You can then loosen the fuel injector line connector at the injector and the remaining air bubbles should be pumped out pretty quickly. Then when you tighten the second connector, be prepared to flip the stop lever if the engine tries to run away or hop around. Yours being a twin, that shouldn't be a problem, but be prepared for anything and always be thinking of what you should do if things go wrong.
As far as the engine running right out of the crate, don't make that assumption. A number of folks on this forum have found the governor linkage didn't move freely because it was glued together with paint. If you take the springs off and flip the stop lever DOWN, the linkage should move freely. Scrape away any paint, and lubricate the linkage with WD-40, a few drops of diesel oil, or whatever you have until it moves easily.
Once you get your engine running, you need to make sure both cylinders are carrying their share of the load. It's common for the linkage between the injector pumps to not be set up right, placing more load on one cylinder than the other. Best way to make sure both are pulling evenly is by measuring the exhaust temperature next to the cylinider head using either a thermocouple probe and a suitable DVM or an infrared thermometer. Play with the linkages until the exhaust temperature is appx. equal on both cylinders and you're on your way.
Next, you will probably have to track down leaks at fittings. The fuel shutoff valve on the bottom of the tank is a troublesome kludge, and the Indian oil filter also seems to leak.
I recently replaced all my fuel lines with flared steel tubing because I couldn't keep the Indian fuel lines from leaking and admitting air after the engine sat for a week or so, meaning I had to evict air bubbles out of my engine weekly. Although the exercise was good for me, it didn't make for a reliable setup.
Remember, these engines aren't a turn-key solution by any means. They're wonderful, funky old dinosaurs, but they take some tinkering with to get them set up right, and if you don't know what you're doing, or if you are careless, you can get hurt or worse.
Best of luck.
Halfnuts
[edit] Properly, the term "runaway" refers to an engine that continues to accelerate even after the fuel is shut off. Sometimes oil can be drawn past the rings, or sucked out of an oil-impregnated air filter causing the engine to take off when you aren't expecting it to. It's a good idea to do your first start with the air filters off and a couple of rags handy that you can stuff into the air intakes, should the engine continue running even after you have flipped the STOP lever up.