Couple of thoughts here. First, if it's just you and your son, then you're in good shape because you're the master of your own itinerary. If you want to stay with an animal or bird for hours, you're free to do so. That's the way I've always done it and it really is a wonderful experience.
In terms of the itinerary, 9 days in 4 parks is pushing it a little bit. I'm heading back in May/June and am spending 14 days in 4. The travel between is wearying, although I'm told the road from Tarangire to the Crater is now paved all the way to the park gate. (Bone jarring is a quite accurate description of the ride.) Bottom line for me: take absolutely as much time as you can. If you can afford to add days, I would highly recommend it. (If not, it'll give you an excuse to get back soon.)
Second, I would be tempted to drop one spot from your list and Lake Manyara would be my candidate. Tarangire will be great for birds at that time of year I'm told, though I'm not sure with the underbrush how much you'll see of large mammals. To drive from Tarangire to the Crater will take a bit of time, but you go right by Manyara in making that trip, so your current schedule calls for backtracking - hence Andy's quesiton. Any time you can free up I would spend either in the Crater or in the Serengeti. And it makes sense, IMO, to drive from the Crater to the Serengeti. It's a bit of a long trip, but at that time of year it should be a game drive trip at the same time. (And I would recommend not taking the detour to Oldavai Gorge, even though it's only about a 1/2 hour drive out of the way.) Our first time there, we had only 1.5 days in the Crater, one full day and one half. That's the standard tour and I think that's a bad mistake. We'll do 4 days there again this year. You may pass the same spot on more than one occasion on all four days and see something different each time. In sum, the only flight I think you'll need to take is from the Serengeti back to Arusha.
Now on the specific questions, I don't have a clue about the wines. Same on the beer, although my son & daughters all prefer Kibo!
Rather than a tripod, you'll want a beanbag for the vehicle. While I've brought my own, all the vehicles I've been in have provided beanbags. Shooting out the roof with a beanbag - when you've only got two photogs - should be easy. Just remember to get low and use the windows as well - a little more difficult with a beanbag but still possible if the bag's not overfull. On charging batteries, I've brought a car charger and that's worked very well for my cameras, less well for my digital wallet where it toasted the charger. The lodges all will have power but you'll need an adaptor. The Crater's Serena was wonderful trying to help me when all my two DWs died. (Tried to FedEx in add. microdrives, albeit unsuccessfully.) If you're both shooting digital, bring a pair of converters, although only one car charger will be necessary. (Check on the power output of the vehicle; I was told that European vehicles have a different output that U.S., but it's not clear what you'll find in your vehicle.) On offloading to digital memory, well that's another story and you may want to start another thread on that one. In the past I've used two Digital Wallets, but they're now out of business - richly deserved I might add. I've switched to a SuperdigiBin, with 40G. Has worked satisfactorily to date, but I'm still contemplating bringing a laptop as well. (Would push my camera-related stuff over 50 pounds total!)
What not to miss while there? If I had one suggestion it would be to take your time. I don't know how many times we would be watching a lion or leopard or ... and another vehicle would come up. They would stay a few minutes and then leave. If the lion or whatever is truly asleep, then maybe it's time to move, but so many times even if they're not actively hunting they will rouse from time to time and you'll have opportunities for good shots. One last suggestion, your guide has primary viewing responsibilities, after all he is the guide. However, he's also got to drive, and I like to stand with my head out the top to get a better view. So my son, daughter, guide and I have had a little friendly competition about who "finds" what. Last trip we saw only one leopard and I was the one that spotted it. (I was the only one with the necessary angle.) You'll likely see more if you really work at it.
I've had a great time going and relish the prospect of returning this summer, this time just with my son. (Only other suggestion would be for you to switch to Canon so that you can trade off on the lenses!
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Rich