the motor and pump shaft need to be set to the same angle. but one either higher or lower than the other so that you have a slight 1-2* angle in your driveline.
what i did in mine was measure how much room you need between the pump and motor with the driveline. you dont want the thing jammed onto the shaft all the way either, leave yourself a good 1/2" or so of room. then i took a piece of 2' pvc pipe and stuck it onto the pump shaft. i took a angle gauge and measured the pump shaft angle. then i lifted the motor into the boat and adjusted it (one of those tilting motor hoist things comes in SUPER handy here) so that the motor was at the same angle as the pump shaft. i used my valve covers since they were flat and double checked with my intake manifold (some intake manifolds have angled carb seats... if so find something else flat with teh crank) with the carb off. then to get the angle in the driveline i moved my motor down and used the angle gauge so there was like a 1-2* angle in the driveline. depending on your boat and your pan you might have to move the motor upwards. make sure you leave yourself some room to get the pan bolt out and so that the pan isnt hitting the bilge. then once its all hanging there in the right spots i drilled and put my rear mount bolts thru the stringer. then triple checked my motor angle and drilled and mounted my front mount bolts. do yourself a favor and get some stringer washers to spread the load so you dont crush your stringers. as far as hardware use stainless bolts with nylock nuts. steel rusts and gets ugly and you dont want ugly in your stringers. you can also put a dab of silicone around the washer to keep any moisture out of your stringer too.