in order to re-align your engine with the C-drive, you need a fixed coupling as on the pictures and drawing.

You don't need to install the shaft alternator pulley while checking alignment. 

Before touching the tools, make pictures and take notes (measurements of all the fittings, position of the nuts on the rubber mounts, position of the engine on the steel cradle, position of the shaft brake disc, etc...).

Start with disconnecting the hoses that could prevent you from moving the engine backwards on its cradle.

Then undo the coupling bolts and the engine steel supports' bolts (attaching the engine on the steel cradle).

Then move the engine backwards enough to remove the coupling bolts.

Then comes the alignment process.

AMEL uses a tool which is a steel coupling machined so that its aft side "enters" the gear-box flange (see pictures and drawing). You can also pre-install the new coupling and adjust the position of the mounts.

First bring the engine forward and make sure the coupling is centered with the gear-box flange, and can enter the gap in the flange. 

Then move the engine a little bit backwards and check that the gap between the flange and the aft side of the coupler is even all around the circumference. To adjust this, you need "thickness wedges" (used in the automotive industry) and play with the rubber mounts nuts to make the gap even.

Then bring the engine forward and tighten the bolts on the cradle and on the mounts.

The advantage of using the tool AMEL uses is that it is easier to install while checking the gaps.

If you need to make one, here's a drawing of the alignment tool for a YANMAR 4JH3-HTE.

The inside diameter (C-drive input shaft) is 35 mm.

The outside diameter is 100 mm.

The diameter of the part that enters the gear-box flange cylindric gap is 62.8 mm, thickness 3 mm.

You should use a VETUS fixed coupling for 35mm shafts, then have it machined to make the 62.8mm "plug" and drilled for the four bolts that should match the flange holes.

The process is the same for Santorins or for Super Maramus.

more info from me: 
* Amel does not sell the alignment tool, I had it made by a machine shop from Aluminium
* I would change also the C-Drive mounts when you change the engine mounts.
* Make sure that the c-drive is "open" and "sits on his rubber sleeve" before you do the engine alignment.
* I used a tool like this to lift the engine https://www.expondo.at/steinberg-systems-kettenzug-2-000-kg-3-m-10030374?gclid=EAIaIQobChMIw9i79ZrE5wIVFuDtCh07Aw33EAQYAiABEgKPs_D_BwE . the job can be done by one person

fair winds, herbert
SN120