I had the same problem, the car would get flooded very easily on startup. Go through the linkage tour here Linkage Tour and make sure yours is setup correctly. Next you need adjust the screw at the back of the pump if it's running rich or lean. DO NOT ADJUST IT WHILE THE CAR IS RUNNING! You will destroy your pump. The pagoda forum is a great resource for the 2.8 6cyl M130 engines. Have a search on there for any issues you are having, it has helped greatly getting my car up and running again. You may also be interested in a series of videos **************.com are doing restoring a pagoda and getting the engine to run correctly here (Mercedes W113 280SL Pagoda Rescue Part 6 - Engine…: http://youtu.be/PLedjKWbU5w) it's only up to episode 6 at the moment.

Also check your ignition timing, if it's out it will cause hard starts. Check the condition of your points in the distributer also if your spark isn't good enough you will be left with unburnt fuel in your oil and blowing black smoke from your exhaust.

Regarding the rough running you need to check through your whole ignition system from coil all the way to spark plug. Personally I'd get a new cap, rotor, points (or replace with an electronic ignition kit) and spark plugs as these are service items anyway, I'd check the condition of the leads and check if the vacuum advance is working correctly.

To check that the fuel pump is providing the right amount of fuel, disconnect the return line on the pump, connect some sort of hose and use a suitable container to catch fuel. Turn the ignition on, you should here the fuel pump buzzing away and you should get 1L of fuel every 15 seconds.

Hope this helps get your car running properly! Feel free to PM if you need some more help