As a rule this is not difficult but it is very important.  Look at your eng. mounts for the adjustments on it. You will need a feeler gauge to ck the alignment, as it must be within 3,000ths.Disconnect the coupling from the trans and slip it back a fraction of an inch , just enough to get the feeler gauge between it and the trans flange.

With your hands ( you may need a pipe wrench for this) rotate the shaft and watch the gap. It must be constant thru 360 degrees, that is within 3,000ths. If the gap is MORE than that an adjustment is needed.

The adjustment can be needed on the coupling or the engine.

If the gap ROTATES with the COUPLING , that is, ck the gap and then rotate the coup. 180 degrees, if the gap moves then the coupling is not on the shaft SQUARE. Depending on the coupling this must be rectified. This is UNLIKELY.

If the gap remains in the same place then you must adjust the mounts on the eng. by way of the adjusting bolts. This requires two people, one the rotate the shaft and the other to turn the bolts SLOWLY as in one half turn at a time. 

Depending on where the gap is , that dictates which corner of the eng you move.

Once all is within specs tighten it all down.