Getting mussels out of the bags is only part of the issue. You also need to make sure there are no large living in low parts of hoses, pumps, parts of the engines, or your water boxes.
Before putting any boat into Lake Tahoe that's been in another lake, it MUSY go through a mussel inspection and decontamination. This is the clean, drained, and dry. During that process every year, they pump 140 degree water up through the inlet and into the bags. Additionally, they also run this hot water through the engines (as you can never get all the water out of the water boxes). On my 242, this means we typically run one engine and fill the water bags, then when we switch to the other engine, we drain the bags.
At 140 degrees, your engines won't be hurt at an idle for the 10 minutes or so they are running but it is hot enough to kill any living mussels or larvae living in the bags, pumps, or pipes.
I also have two 400lb bags that we use on the boat as well. For these, I remove them from the boat, open the fill valves and hang-dry them in the garage for a week. the pump I use also gets hung as well.
So the challenge becomes how to either get hot water through your systems or find a way to drain them... Maybe some of the people on here may have an idea on how to pressurize your hot water tank drain or put a spigot on the pressurized side of your hot water tank?