How NOT to launch the Mac mini into orbit

There are several steps to successful dockings. Click on images for larger view.

1. Set your target as your target.
2. Time your launch: A general rule of thumb is to launch when your target is just rising in the west (unless your target is in a retrograde orbit). If your target isn't in an equatorial orbit, then you'll also want to launch when the orbital plane crosses your launch site.
3. Launching: this is pretty standard. One key thing to remember is to set your apoapsis to meet your target altitude. Circularize as per the next step.
4. Closing the gap: if you're leading your target (in front of it), you'll want to increase your orbital period. Burn prograde to increase your apoapsis about 5km higher than your target, or until the intercept minimizes. In a similar vein, if you're trailing your target, you'll want to decrease your orbital period by lowering your periapsis. Also take this time to make your orbits co-planar by burning in the normal or anti normal direction at the descending or ascending node respectively. If you're already within about 5km, you can skip this step.
5. Initial approach: by now, the nav ball should be in target mode. In this mode, your velocity vectors indicate the relative velocity between you an your target. Keep your prograde vector pointed at the target, and reduce your relative velocity to under 50m/s. As you close in, continue making adjustments to your course to keep your velocity vector on the target indicator and continue reducing your relative velocity.
6. Final approach: by the time you're within about 1km, you should have a relative velocity less than 10m/s. Hopefully you remembered to orient your target ship such that one of the ports is pointing north or south (for equatorial orbits, normal or anti normal in general). Point yourself in the opposite direction, thus making the axis of the two docking ports parallel. Now you can switch to docking mode, as you don't want to use your main engine anymore. Change your view to Chase by hitting V a few times. Now use translation controls to line up the axis of your docking ports, thrust forward, and let the docking ports magnetism do the rest. Just not too fast. Keep it under 1m/s within 10m.

As a side note, I screwed up this particular approach because I wasn't paying attention and didn't reduce my speed as I closed in. I shot past the target ship and had to correct. Additionally, you'll note that I didn't in fact change to docking mode. This is a personal preference, and I use both hands on the keyboard to control my attitude with my left had (WASDQE) and translation with my right hand (IJKLHN).

So you're correct in using Jool for a gravitational slingshot into a high inclination, and you're also correct in assuming that you can only get about 40° from an encounter prior to switching the spheres of influence. Trying to set up burns prior to switching SoI is an exercise in futility. What you do want to do is set up your encounter so that you're coming in close to over a pole. 200m/s early (about a month out from switching SoI) can save a lot down the road.

Getting your trans-Joolian burn correct is actually one of the biggest factors for saving fuel. Not only do you minimize delta-V on the transfer burn, but you'll also minimize delta-V on the polar injection burn. You want to start your transfer about 65° after crossing the terminator into night when Jool is leading Kerbin by about 95°. When it comes to the phase angle, burning too early is really bad, as delta-V costs go up exponentially with the amount of time before optimal. Burning late isn't so bad, as costs go up much slower (quadratically maybe? Don't know for sure). This is a utility for determining optimal burn patterns.

So you've done your transfer burn, and you've done your final correction burn before switching SoI, and you're just waiting those last few seconds before that Jool orbit line changes from yellow to green. When that happens, you'll want to immediately plop down a maneuver node not too far in front of you. You're basically going to be doing a bunch of min-maxing to get your inclination into the high eighties. First, set your incoming inclination for best result inclination. Next, add about 500m/s of prograde velocity. You're doing this because you essentially have to kill something like 4000m/s of horizontal velocity and turn that into vertical. Next, reduce your periapse using the ground vector until optimal. Rinse and repeat, adding the most velocity in the prograde direction. Eventually, you'll get to a point where the inclination of the resulting orbit is correct, but the periapse will be in the sun, or the apoapse will be way out of the system. You're three options are to try and fix it now, try to fix it at Jool periapse, or (easily) fix it once you achieve polar orbit.

It's a tough operation, but with patience and experimentation, you should be able to get it every time.