Engine makes a knocking noise when in neutral .... what could it be?

A couple of months back I replaced my PDS bearing because it was shot. Everything was fine for a couple of weeks. All of a sudden the engine ( I think its coming from the engine) started making what sounds like a knocking noise when the boat is in neutral. The u-joint snap rings seem to have gone in just fine. I'm going to remove the drive shaft bellows and make sure one of the u-joint caps haven't come loose.

At first I thought it was my water circulating pump going bad, so I replaced it. The noise was still there after replacing it, so it appears that wasn't it.

Could some other bearing be the cause of the knocking noise? When in drive or under acceleration the knocking goes away and the boat appears to have no issues. It seems to be getting worse and worse. I don't want what ever the cause to go bad at the wrong time.

In case my signature doesn't show my drive or engine model, I have a 1994 5.7 GI mated to a AQ-C drive.

I pulled off the drive bellows and noticed at least one of the snap rings holding one of the u-joints had come off. Also, I noticed that one of the u-joints, possibly the one that the snap ring I found had come off of, was even with the outer edge of the cross members that hold both u-joints.

Obviously not a good situation. Am I going to have to remove the transmission and PDS shaft to get the u-joints seated properly again? Or will I be able to just remove the transmission?