If its a 1000 series fastram perkins timing marks should be on the gears, key way in crank shaft gear should be more or less striaght up.
New pump should already be set a top dead on number 1 (locked with bolt in side of pump)
you should be able to see where the old pump key way was on the old hub as they normally leave a very slight mark even though they are not keyed to hub.
If you have the 1100 series perkins i remove rocker cover set valves of number one on the rock then use a drill bit which goes through a hole in block to lock crank shaft. lock up fuel pump with lock bolt on side and pump is set a number 1 top dead. take it off do what you have to and refit.
All new or refurbed pumps should be set at number 1. if you have lost this setting you should idealy take it to diesel place to get it reset, if your lucky you can remove locking bolt look in hole and you might see a mark on the shaft where it was locked before.
with the timeing cover off look at the gear for the cam, it has one small hole that hole must be rotated till it sits at about 3 oclock. put a drill bit in the hole, is should go in more then 1 inch. that will hold the gears in the propper place for you to put your rebuilt injector into. there is no need to take off the valve cover to do TDC, perkins has built this little hole in the gear and block just for this purpose.