Here is a short list.
Check for the reverse gate not going 100% open.
Check that the ride plate did not get over torqued, this will allow air to be sucked and and do some weird stuff.
Make sure all the bolts are in the right place and none missing.
Check out the exhaust seal near the transom, this keeps the exhaust gases from being pulled into the jet unit..
I have some buddies that race these things on rivers, I will post your question on the other forum...

BTW, Thank you for your service.

Wish there was more I could do.
GT