...... 2)I've never done a jetski engine (though I have done a jet engine)....
I'll go straight. As I understand it from other posts, its a pump housing that has a long sliding shaft and you adjust the engine till it slides in straight. The pump shaft can't be used as the end is round (I suppose to be a mini-CV joint for minor differences).
So any suggestions?
For #2... doesn't mater. Big and expensive engines are a different breed. Not to mention... if you've played with a turboprop... the secondary stage will either be a secondary turbine (not needing alignment) or it will be a continued shaft, that will have a gear, and a machined case to do the alignment for you.
Yes... you really can't use the pump and shaft as a tool because they do allow for a slight miss-alignment.
Your "understood" method is correct... but you also shim the pump. This is where the second issue is at. So... if you think someone removed the shims... it makes it very hard to align without the tool. You may get it close enough that it doesn't bind when all the bolts are tightened down... but the farther off center you get... the faster the parts will wear. I've seen it a bunch of times, were guys think they have it right, and then all the sudden, they rip the splines out of the PTO, or the bend a driveshaft. (causing major damage)
I'm not trying to be harsh... but the answer has been given. SO... it's your ski, do what you want. BUT... there is a high probability that you will have a problem (Eventually) if you don't use an alignment tool.
I know you are out of the USA... but I'm sure if you look around, someone will have a tool you can use. The price of the tool, or to pay a shop to do the alignment will be less $$$ than the potential repair costs. (Damaged PTO, Bent shaft, damaged impeller, damaged pump housing, busted hull from the driveshaft bending while it's spinning, or a busted crankshaft) This falls under the category of do it right the first time, or spend the $$$ to do it the second time.