I just attended a fantastic presentation on Juno last night at Purdue University, by a young woman alumnus, now a JPL engineer on the flight dynamics team for Juno. I had many of the same questions you do, and learned some interesting things!
Regarding the burn to go from the 53 day capture orbit to a 14 day "science orbit," indeed it didn't happen yet, because of concerns with a check valve not operating as quickly as it should (minutes not seconds). They're still studying it. The current orbit is a good one, just a bit slow. They might do a lower power (lower ISP) burn at some point and put it into a 21 day science orbit using the engine in "blowdown" mode, where they don't pressurize the propellant tanks, and sidestep the check valve issue. But that's just one option they're apparently considering.
Jupiter, as you probably know, has a daily rotation of about 10 hours and has a pretty pronounced oblateness...so there is a substantial "J2" term in the gravity model of the planet; it can't be treated as a point mass at all times. So during the close-to-Jupiter, perijove part of the orbit, the J2 effect changes the orientation of the orbit. This is well known to those who follow this mission, and was planned for. What it means, is perijove, currently closer to the equator, will gradually move toward the north pole after several orbits, and the high point (apojove) will move further and further south. Why does this matter? The orbit was planned to avoid the intense radiation fields surrounding Jupiter like a doughnut. But due to this orbit shifting effect, eventually the probe will be flying (during part of its orbit) through some pretty intense radiation, off its original path that minimized radiation dose. So toward end of life, she said Juno will have had something like the equivalent of 100 million dental x-rays.
They always plan any orbit changes (burns) to occur when the icy moons (Europa etc.) are as far away from potential harm as possible. Apparently they're obeying the Monolith. They also plan to de-orbit, at end of life, into Jupiter itself, which is apparently relatively OK. (Although my wife points out, we're now contaminating Jupiter with Earth microbes, but maybe they're not expected to survive.) One option they've considered for EOL is to maximize science near the end: lower perijove to skim very close to the north pole, maybe a few hundred km. Then as the orbit naturally shifts perijove to be more and more south, eventually the probe, even if uncontrolled at this point due to electronics failure or lack of fuel, will eventually hit that equatorial bulge around Jupiter and deorbit. That's pretty good flying.