Pump - engine alignment

[Lugnut]

Purchased somewhat of a "basket case" 91 X2. Starts & runs badly (Chitty Chitty bang BOOM). Everything under hood is no mystery, I got that but the pump engine alignment, that's another matter. Don't have a clue where to start. Took a page out of the Sea Doo alignment procedure & fashioned a sleeve which inserts into shaft tunnel, slip fit into tunnel, slip fit over shaft = dead center. Is this where I base my alignment? Is that tunnel true to either/or? If not, Where is the "true" component/ position that I base the alignment from. Snap shot of where I'm at.
Shaft straight & true but missing material. No mystery there, replace.
Shaft bearing loose & hanging. Bearings are trot line weight
No shim(s) @ motor mounts. Motor mount "appear" to be in good shape.
No shim(s) @ pump.
Coupling rubber good.
All evidence points toward that the motor/pump was pulled by previous owners & assembly was done in "Half Measure". That alright, I knew I was purchasing a basket case.
So knowing this. The procedure of alignment starts where? Maybe @ the coupling with precise measuring of gaps/distance or is that measurement reserved for validation? Hell, I don't know. Engine/body/electrical on PWCs I know. Pump- engine alignment, not a clue...
Please help.
Pics with parallax. Shaft favors 12:00 o clock straight up.

 

[Myself]

What I do on any of the finger style coupler setups is this. Bolt the pump up snug. Insert driveshaft making sure nothing feels like it's in a bind. If it is....you have to unbolt the midshaft or bearing holder and re-center...OR shim the pump. When it feels like nothing is bound up then set the engine down in and shim the mounts until you have aligned couplers with the same gap top/bottom/sides.