WaveDemon is right, pump alignment is very important to minimise spline wear.
The majority of pumps in skis are never set up with perfect alignment, they are just bolted in.
Take off the mid shaft bearing housing from the bulkhead.
The prop shaft should sit exactly in the centre of the hole in the bulkhead.
I machined a sleeve that slides over the prop shaft & into the bulkhead.
The sleeve should slide back & forth easily - this will ensure correct alignment.
If the prop shaft is not centered, loosen the 4 pump bolts.
Remove all shims.
Adjust bolts left to right, front to rear, until prop shaft is in the center.
At least 1 bolt should be firm by this stage (pump foot sitting against hull).
Check the gap between the pump feet & the hull on any of the pump feet that aren't contacting with the hull.
The gap measurement is the thickness of the shim that is required for each pump foot.
Put in shims.
Tighten pump bolts.
Finished!
PS. if you have to replace either the prop shaft or middle shaft with a brand new shaft, don't just replace one, you must replace both.