What I think you're looking for are specific spots/waterholes that are not too bad, and relatively quiet... Well, I have done Kruger north to south in December, and I have been looking more or less for the same spots. This is my recommendation.... This is only if you're not a big5 'hunter' and appreciate any sighting and have no problem with tough dust roads.
South:Hard to find a quiet spot, however I found the s25-s108-H5 loop, just north of the s25 quiet a good piece. Nice and quiet.
S65 is not that busy, also a good road!
Furthermore, the s36, especially up to Jones /Lugmag Dam as well as the S33 Vutomi road..
I personally found the s37 not to bad either....
Central:The s39 (southern part) is quiet, not that many animals but very scenic! And you never know. s39 (northern part) is very good!
The s47 Tzendze loop North of Letaba is teaming with wildlife, and relatively quiet.
The Road to Mingerhout Dam is also very scenic and lots of animals around.
North: Road to Stapelkop dam west of Mopanie is long and tough, however the dam is extremely beautiful and I personally have seen lots of animals there!
Thiyongeni loop is a MUST in the afternoon, although there will be a few cars around, it will never get extremely busy. VERY good road, one of the best in the park!
S52 dustroad towards Bateleur from Shingwedzi, awesome loop and nice and quiet. Red Rocks and Tsanga Outlook for the view and peacefulness.... ALSO A MUST DO!
s56 Mphongolo loop, extremely beautiful and there is always something around. relatively quiet. My favorite loop in the park.
Mahonie loop and loops to Klopperfontein are a must.... always something to see, very scenic and quiet.
Extreme North:The s63 dustroad loop is quiet after the picnic spot, and a must visit.
Hope this helps, and remember: @ the right time @ the right place.... My best sightings have been on the more quiet roads....!