Which point do you check timing at?

I use point A.
I'm having some serious problems here.
I tried to check my chain stretch but my cam has code 11 on it. I can't find any information on this code so I decided to use the cam tower markings instead of the usual 2mm valve lift method. Doing this I got 4 deg stretch.
Now I decided to adjust my injection pump. I used the injection pump holding tool for this. You set the crank to 15 deg ATDC minus chain stretch, so I set the crank at 11 deg ATDC on compression stroke. Put the tool in adjusted the pump. Tool popped in and set the timing. Put everything back together and it runs like crap!
It was bouncing at start up and barely stayed running. lots of smoke too.
I don't know what to do now.
I'm thinking about putting the crank to 15 deg ATDC and setting the pump back to the way it was. Other than that I'm completely at a loss, other than take it to an Indy but I really don't want to do that.
Any input would be greatly appreciated.
Danny