to tell or not to tell: major revisions

With my first novel, I queried only a few carefully-selected agents and I finally began getting some requests. I made it as far as a Revise and Resubmit that ended up being a rejection, but I received some very thoughtful feedback from that agent. Since then, I have carefully studied that feedback, feedback from the other agents, workshopped the story with a creative writing teacher/freelance critiquer, and made time to read similar titles in my genre. Collectively, I got it. It clicked and I understood all the feedback, realized I had queried too soon, and that a major edit was in the cards. I'm talking taking it down to the studs, recognizing that I was working off the wrong inciting incident and starting the story too soon, making my hook stand out, cutting out as much as 15k words to rejuvenate the pace, and switching to a stronger title, more reflective of the high speed/low drag version I am shooting for. In the end, none of these revisions may garner any more attention for the story but it's not a total loss because I have learned a lot from the process. When I am ready to query again, I would like to try again with some of the agents who had rejected my original version. Some have said they are open to requerying with major revisions and some haven't said, but like a great shark I know always says, the worst they can say is no (again).

Now, my question: In my new query, do I fess up that they have already seen a different version of the story but that it has been heavily revised based on agent feedback/professional editing or do I just treat it as a brand new query so as to not bias them?

I realize it's delusional to assume they'd remember me or my story anyway when they receive hundreds of queries a week, but I don't want to be flagged in Query Manager as submitting before and the agent say, "OMG this jerk is trying to slide in old garbage under a new title!" and it be an automatic rejection. What is the best way for me to proceed?

Let's remember my purpose in reading queries: to find good stuff that I can sell.

Clearly you had a good start on this, but didn't make it to the final round.
Do you know how many Miss Americas try more than once?
(me neither, but it's a lot)

So, yes, query, even the ones who passed.
Say what you said here (but more concisely).

Make SURE those first pages are razor sharp.
When someone requeries me for a novel I was interested in earlier, I always read those pages to see if they hook me.  A flat start (backstory, ruminations etc) gets a quick pass.

Get me with those first pages and I usually request the full.
I NEED TO SELL THINGS!

I can't just sit around saying "oh she queried before, pass!"

The whole thing about requerying is to do what you've done: take it down to the studs and start over.

The things that are more likely to get a quick pass:
requerying without enough time passing. Revision takes time. Not just to write, but to think.

Changing only surface things.
 "I fixed the places you pointed out" means you didn't fix the places I didn't. And no one gets a full edit on a requested full. No one.

The market or my interests have changed since you queried.
That's a hard one, I know.

Any questions?