If you decide you don't want to drive in the Cotswolds (though I don't know of any reason why you shouldn't), I enjoyed my one-day van tour run by GoCotswolds. It picks up at the train station in Moreton-in-Marsh. I think the Secret Cottage tour does, too. I stayed in Oxford for several nights, and it's easy to take the train from there to M-I-M for one of the Cotswold tours. More convenient for your current itinerary would be the MadMax Cotswold tours that depart from Bath.
You've mentioned a couple of pricey London sights that are on the current 2-for-1 list. The list of participating sights, and date exclusions, can change, but it would be worth checking your itinerary against the information on the website to which I've linked. Buy one/get one free is a very nice deal. I don't know how well this would work at the Tower of London, which I believe has very long lines. You might decide you'd rather just buy tickets in advance (assuming that you can: I haven't checked) and forego the potential savings to avoid time wasted in line. But I've never heard of a significant delay in the ticket line at Kew Gardens.
As I understand it, taking advantage of those 2-4-1 deals requires that each of you have either a train ticket into London for the day in question or an Underground travel card purchased at a regular rail station (not an Underground station). This subject has come up often on the forum; you can find more information by using the Search function.
It appears that you'll have several rail trips that can be much, much cheaper if you snag Advance tickets shortly after they go on sale; I understand that usually happens 11 to 12 weeks before the travel date. I recommend checking nationalrail.co.uk now to see which travel legs have prices that vary a lot, depending on how early you buy the tickets. (Compare prices for travel tomorrow to Advance ticket prices for May.). The savings can be huge--way over 50% for some routes. The Advance tickets generally tie you to a specific date and departure time. You may be able to make a change later, but there will be an administrative fee and you'll have to pay the difference between your original bargain fare and the current fare for the new ticket, so a last-minute change will probably be very costly. Best to be sure of your timing before buying any rail tickets.