Pruning a couple candles right after repotting is no big deal. In general, especially with pines less vigorous than Pinus pinea, one usually allows the tree a full growing season to recover with zero pruning. De-candling and pruning the following year can cut back more than one seasons new growth.
You can wire the tree in late summer or early autumn. Wiring is not as stressful on a tree as pruning.
About nebari. Often the beginner mistake is to expose the nebari too soon. The nebari should be buried while in development. It is only exposed when the tree is moved to its "exhibition pot". In general the nebari should be covered by at least 1/4 inch of media, roughly a half centimeter for metric folk. If exposed too early, fine roots will dehydrate and die.
About your knee. Next time you repot, cut that entire root off flush at the trunk. It will never "flatten out" and will usually be considered "ugly" by most bonsai observers. If you like the look, that's okay, but if you still think it is ugly when you repot. Cut it off flush at the trunk. If the wound is buried at least 1/4 inch or a little more under the media, it will be moist enough to sprout new roots at that point. Do not use any sealer for the cut wound.