Number 1 is at the front of the engine, where the water pump and alternator are located.
I can't even say you can tell by the smoke if you removed the exhaust manifold. Especially if its an east/west facing machine.
As for torque, i haven't found this to be an issue, ONLY tighten it by the body, not by the part that holds the internals in, remove the tap off fittings and use an extended socket to tighten it up. Install new copper washers, these should be supplied with the injectors. Replace the tap off banjo fittings and aluminum washers and nut, install the the tube lines and you should be set.
As for the injector pump, you would need to take it to an injection shop, they can attach a gauge to check delivery pressures and that the valves are working correctly. This is all done on the machine, don't remove the pump!. If its smoking i'd suspect the injectors before the pump, if the pump was going i'd expect lack of power but not excessive smoke as fuel delivery would be lower than it should be. But i am not a diesel mechanic.
Personally i'd clean around the injectors by un-doing them a few turns and then blow the junk out from around them with compressed air. Finish removing the injectors and delivery tubes. Attach the shortest tube to number 1 on the injector and put an injector on the end of the tube. Keep it pointing down and away from you and get someone to crank the engine over. Check the spray pattern, repeat for the other 3 injectors. Remember the tip of the injector shouldn't have any droplets on it, thats a sign of leakage and the injector needs a re-build. Only crank the engine for small bursts, like no more than 20 seconds and let it cool. There won't be a lot of load on it, but still go easy on it.
Keep where the fuel injects into the injector as clean as possible, the tap off section isn't as critical but keep it as clean as you can.
I pulled down 4 sets of injectors and cleaned them up and tested them this way, they ran sweet as, no smoke at all, not even at startup!!!. If you pull them down, do only 1 at a time, never mix parts from different injectors up. Be careful not to damage the nozzle on the injectors, they are very fragile. If you need any help just give me a yell.