Obviously driven by the ads to destroy your actual assets
You didn't mention the two most obvious changes I've noticed so far. You increased the visibility of the ads and made the overall effect more intrusive (and therefore less attractive) and you made the comments less accessible (and presumably more controllable AKA easier to censor).
What are your actual assets? I think you have two: Integrity and credibility. Rewording as questions, do you speak the truth, and do we believe you when you speak? Showing how much you worship the ads damages both of your actual assets. The probable result will be fewer eyeballs for you to sell, resulting in lower revenue, resulting in greater desperation, resulting in a death spiral. Nothing special there, looking at the state of Web-based journalism.
Hey, why don't you try a different business model? Here's a version of an ancient suggestion adapted to your situation: I call it #MDFC (More Democratic Funding Campaigns), but you might prefer to think of it as "better than Kickstarter". Essentially, you would EARN a commission by supporting constructive projects related to your stories.
For simplicity and because the Register isn't worth a lot of effort for customization, I'll use an example based on a problem. A hot one right now is Web neutrality, eh? After an article on the topic, you would offer 3 to 5 links to #MDFC projects to help SOLVE the problem. You would earn your commission (let's say 5%?) by supporting the project proposal and EVALUATION of how well it worked. You would make sure that each proposal is complete, including a feasible budget and schedule for ALL of the required resources. You would work to make sure (based on your increasing experience with prior proposals) that nothing crucial is omitted, like testing or the cost of a satisfaction survey. Most importantly, you would make sure the project has clear success criteria. If enough of the readers like the project and pledge money, then you would fund the project (and take your cut) and afterwards, you would evaluate it. (By the way, a project might be internal, such as additional research and another article on the problem.)
Where does the money come from? You can hold it by acting as the "charity share brokerage" and we would trust you to manage our "charity share brokerage accounts". After we pledged all of our donation to various projects, we could look back at our donation history, see how much good we had done by helping to fund those projects, and hopefully decide it's worth another donation.
Convince me you're interested and I'll reveal some of the viral funding aspects...