Nice trip you have planned! Only 14 days only for all that? You'll be back! Also good to see I have been booked for the 12th, and I am really looking forward to meeting up with you!
Can't help you much with Namibia, but here's some tips for your SA leg:
Cape Town:- In Cape Town you can get a room in a 5 star boutique hotel for much less than your budget. Prices are often better for local travelers, so more than happy to assist in any way here. It is nice and central ito the attractions around, and even the city center is a pleasant experience.
- Boulder beach is a short trip, and I would suggest you take a day and do a loop around Simon's Town, (Boulder Beach), Cape Point, Chapman's Peak Drive, Hout Bay (stop here for lunch), Llundudno, Clifton and then back to Cape Town. Try to get back to Cape Town in time to take a late afternoon trip up Table Mountain by cable way to watch the sunset from there. May is not ideal as it can be quite cold up there, but the view is amazing. Alternatively head out to Table View, have dinner at the Blue Peter and see a spectacular sunset from there (the most famous view of Table Mountain is from this vantage point).
- Franschoek is a great day trip too, overall not quite as scenic as the Boulder Beach one, so if you are pressed for time head out to Stellenbosch, and from there travel directly to Franschoek over Helshoogte Pass. Alternatively you can do a very nice loop around The Strand, Gordon's Bay, Franschoek and back to Stellenbosch, but for that you'll again need a day.
- If you are into wine tasting, Stellenbosch is a nice central point as it is surrounded by wineries. Another option is to head out towards Robertson which is a bit further out but also has some first class (less commercialized though) wineries surrounding it.
- Sadly time will not permit you heading up the garden route, but certainly remember that for your next visit!
Kruger:
Not much I can add here, other than I feel your pain as it has become a very expensive destination. Again, it is slightly cheaper to book as a local, so remember that for your next visit! Your choice of Hamiltons will certainly win you many brownie points with the Mrs!
Please remember that in late summer there still is risk of malaria in that part of the country, so be sure to start taking malaria tablets well in advance of your arrival!