A few points for you to bear in mind:
i. You absolutely must find the 15˚ or 13˚ timing mark. (depending on newer or older series 3s) is there, but can be very faint. Access isnt great but I found if you remove the inspection cover and lie across the engine left to right you can poke your head down into a small recess where the air cleaner usually sits. Use a torch and have your friend crank the engine very slowly (clockwise). On mine, the timing mark came quite soon after the EP mark, when turning the engine in the normal direction of rotation.
ii. Remove the pump and check that the master spline sits at 20˚, as specified in the workshop manual. If the master spline is much further from the horizontal than 20˚ let me know and there are two possible options I know of for you.
iii. Now you will need the timing tool to ensure that the backlash in the gears is taken up. Its possible to make your own tool using a packet of quick steel and proceed as follows: Mix the length of quick steel thoroughly and take the vertical gear drive shaft out from the drive gear. As the quick steel starts to go off, you will feel it getting hot, roll it into a thick cylinder. Now press the pump end of the drive shaft into the end it so that the imprint of the splines is left in the quick steel. DO NOT leave the drive shaft in the quick steel as it hardens as it will bond and youll have a bad time trying to extricate one from the other. When you have obtained a good fit between quick-steel and drive-shaft let the quick-steel harden. Then cut a flat onto the other end of the quick-steel such that you will be able to turn it with a suitable lever. I super glued a wooden lever onto mine.. To use it, engage the drive shaft onto your tool, and place the whole lot into the vertical drive gear; the end of the tool should be protruding form the engine block
iv. Now use your tool, turning clockwise as specified, to take the up the backlash in the gears..
v. Now remove the inspection window on the back of the pump and align the timing mark A with the circlip inside the pump and mate it (the pump) to the drive gear. Proceed as directed for the older type injection pump in the Haynes guide. If you havent a copy of this let me know and Ill forward you a copy of the relevant pages
This worked a treat for mine; Id say I was as bad off, or worse than yourself. Since carrying out the above job I have about 30% more power and gone from clouds and clouds of blue smoke to none. But forget about grinding new holes on the pump body, and making minute changes to the positioning of the pump body. Remember it is the positioning of the INSIDE of the pump which, relative to the positioning of the engine which is what is important. Drop me a line if youve any queries, good luck, youll get it there shortly
Pat