The engine had never been removed from my GSX. When I bought it, I had the drive out so while i was at it, I checked the engine alignment. I ended up shimming the entire engine up, & even more so in the front to get it perfectly aligned. Now I recently picked up another project. this ski has every original oetiker clamp on it (except the carbs), so I am assuming the engine has never been out either. I'll check the alignment, & I am going to guess its not exactly where it should be. So, I would even go as far as too say even the untouched ones are probably not perfect, then if you take things apart it only gets worse.
Now that I invested into the tool, I really can't see another way to do it. My first ski I bought with the engine in a box. I used every thing I could think of to align the engine & It still had a vibration. Bought the tool, & found I was not very close with my survivor method.
I would at least consider what was suggested by a member here last year. Have a machine shop cut a shaft for you & slide it though your mounted pump housing with the impeller shaft removed. We can give you the sizes if you need them.
The pump housing allows the shaft to wiggle a little more than the tool does, but will still get you where you need to be at an economical cost.