Make sure you have a set of flat metal feeler gauges in that cover up to 0.250" in 0.001" increments (you should have these for valve setting anyway);
Use a proper
marine engine-propeller-shaft coupling (flange type);
Make sure the engine has vertical alignment (leveling) screws - much easier than trying to insert shims;
Position the engine close (within 0.010") to the coupling flanges for "gross" alignment;
By means of a file or centerpunch, mark each flange rim at the "common" coupling bolt hole if this has not been done by the manufacturer. Much easier to reassemble coupling at later dates;
Sliding the propeller shaft in/out, use the alignment screws and a small "bar" to bring the flanges to within 0.004" max. separation of each other, measured at the rim of the flange and in alignment with the flange bolt holes;
Locate and drill mounting bolt holes. Use "engine hanger bolts" (lag screw threads on bottom, machine screw threads on top) for easier adjustments - now and later;
Finger mounting screw nuts;
Raise or lower alignment screws to maintain the correct flange alignment - faces should not vary more than 0.003" overall and insert metal shims between the engine bedplate and the engine bearers. I usually mount a strap of flat, 1/4" steel on the engine bearers running the full length of the engine bedplate; wide enough that the engine weight is carried entirely on this strap metal.
Most decent marine engine mechanics can show you/sell you what you need to do this. Trust me, a couple thousands off and you'll know.