One thing I want to point out when aligning an aftermarket hull... When guys aligned a stock superjet, they just eye balled the driveshaft coming through the bulkhead and tried to get it center. You can't do that with an aftermarket hull because the hole in the bulkhead is totally arbitrary. You HAVE TO install the pump and then slide the midshaft over the driveshaft without it hanging on the driveshaft (because hanging the midshaft will bend the driveshaft down slightly) and see if the mounting holes line up. Then shim the pump accordingly until the midshaft holes line up.
BTW, I hammer the throttle every time I enter the water after a jump and have been doing that for years. I'm running a big bore with total loss so I'm spinning the engine up pretty good before it gets shocked as it hits the water. It's brutal on the driveline but that can't be your problem because I haven't had a problem yet.
Thanks waternut! I'm headin to my shop now so that'll be the first thing I look at when removing midshaft first