Has anyone had this issue? What did it sound like? Similar to rod knock or pushrod tapping but obviously coming from the bellhousing? How did you determine this was your issue?

Does the engine have to come completely out or can it just be lifted?

Easy - It would vibrate like its out of balance.

The first thing the starter would NEVER engage.

Why would you think it loose bolts?

I disgree with bigjim. I have had a flywheel come loose before, and it would start right up. The sound it made was that or a knocking rod. Once i got on the bolts, they were just slightly loose.

Definately check the flywheel before tearing the engine down. Im not sure about removing the engine or not, im sure someone will be able to comment.

Yes it does make a knocking noise. Just like a cracked flexplate.
The 2 that I have heard were on front wheel drive cars. And as stated earlier they were a little more than finger tight.

I have a tapping sound that is coming from that area (very back of the motor and dead center)...I had the motor rebuilt in late 2009 and the shop had to take the motor out a couple times to troubleshoot an issue I was having. It seems like that may be my issue. Was just curious if anyone else has ever had this issue before and if the motor has to come out to tighten them down....

Well it's like this. I'm going to assume it's an Alpha or Bravo since you didn't say. First the drive will need to come off. Then everything will need to be disconnected as if you were going to remove it from the boat. Then it will need to be lifted some and shifted forward. At this point you could remove the bellhousing and coupler and tighten the flywheel bolts with it hanging there in the boat. This being said I don't know if there is even room to move it forward any in your boat. Maybe can turn it 90* while hanging and work on it. Personally I would just lift it, pull the boat out from under it and then let it down to the ground to steady it and work on it there. Should only take 20 minutes to check and tighten them and be ready to go back in. Lifting it and doing it in the boat would be unstable trying to torque the flywheel bolts to I believe it's 70 ft. lbs..

Yes, its a Bravo 1 drive. Yeah, I figured the drive would have to come off and the engine would have to come out. Great!