I have one experience somewhat like this so I can help you out to a point.
I was working on a Perkins diesel in a MF 750 combine. I needed to replace the front engine cover and while removing a gear the engine turned and all my carefully set timing marks were useless. So with the verbal help of a diesel shop I got everything back together.
First I found top dead center TDC on the engine by installing a socket under a rocker for a valve (doesn't matter which one) on number 1 piston. Basically you just want to hold it open. Find a pointer on the front cover or make a mark on the front cover. Next you carefully rotate the engine until the piston touches the valve inside the engine. When the piston touches the valve you make a mark (Use a piece of tape or something that is removable) on the front dampener pulley beside the mark you made on the front cover. Then you carefully rotate the engine in the opposite direction until the piston touches the valve again and make another mark on the dampener pulley opposite the mark on the front cover. You should now have 2 marks on the front pulley. Half ways in between those 2 marks is TDC. Carefully measure the distance between the 2 marks and divide it in half. Make a more permanent mark on the front pulley exactly between the two marks and then remove them. You don't need them any more. Remove the socket on the rocker arm as you don't need it any more either. (If your dampener pulley is already marked with timing marks then you don't need to do the above exercise.)
Now you need to go to the diesel shop and ask them to tell you what the timing is on your engine and ask them to set the timing on the injection pump to that specification. Or even better to show you where the timing marks are.
Once you have that info then you can get back to your engine. Now if there are no timing marks on the front pulley then you need to make some. Get a metric seamstress tape measure. Believe me this is way easier in metric!! Wrap it around the front pulley and record that measurement. Say you get lucky and the measurement around the pulley is 360mm. That means that every mm is one degree of rotation. Say the timing on your particular engine is 7.5 degrees. You measure from the timing mark you made on the front pulley 7.5 mm against the rotation of the engine. You want to turn the engine backwards to make this mark as timing is before top dead center. (BTDC). So you aren't lucky and the measurement around the pulley is 245 mm. The math goes like this then. 245 divided by 360 = .6805555. (360 is the degrees in a circle) Next multiply .6805555 x 7.5 degrees = 5.1 mm. So 5.1 mm back from the TDC mark is your 7.5 degree timing mark. Once that is done you line up the 7.5 degree BTDC mark with the mark on the front cover.
Now install the pump making sure all your timing marks are aligned. Also make sure you get diesel fuel into the pump before you start cranking the engine over to start it.
This is all a pretty involved procedure for an amateur mechanic. It would be nice to have the help of someone who knows what he/she is doing. Good luck.
Edited to add that if thepumpguysc get involved with this your in good hands. They are a lot more familiar with this kind of problem than I am.
