Hi Peter, quite a history you have.
It looks like you have a lot of good advice above, but I want to add a little to what Josh said. I think you are correct to clean up the site, these things will bite you eventually, but it would probably make sense to do it in a staged approach. By cutting off a bunch of pages that rank, you are unfortunately going to lose a lot of traffic, that doesn't mean it isn't the correct long term solution, but the situation you've found yourself in now is as bad as a penalty.
If you are not getting a lot of traffic from the redirected domains I would recommend removing the 301s too, eve with the disavow file I would be concerned that it could be causing issues, especially as such scale and such a variety of topics. I don't see how redirecting a generator hire website to a cleaning website is relevant at all, I suspect Google see it the same way.
To summarise, if this change is costing you money, I'd reverse it, but start planning to get to the point where you can remove the pages asap without the same level of drop, at the moment you've essentially given yourself a penalty.
Best of luck