The short answer is that the shortest real-time orbit will always be at the altitude at which you can use the maximum time warp. On Kerbin, going from the lowest possible orbit (70km) to the orbit at which you can use max (100000x) time warp (600km), will increase your orbital period from 1834 seconds to 4395 seconds (240%), while the time warp available increases from 50x to 100000x (200000%). This means that an orbit at 600km will take approximately 0.1198% of the real time that an orbit at 70km will take. While the exact numbers will vary on different bodies, I feel confident in saying that the altitude for max time warp will always be the fastest real-time orbit.
In order to calculate this I used the advice in this tutorial. I used the masses of Kerbin and the Mun from that thread, as they were pre-formatted in the proper manner*. I then entered into Wolfram Alpha orbital period <mass> <equatorial radius* + orbit altitude> e.g. orbital period 5.2915793*10^22 kg 840 km. This allowed me to find the orbital period at each minimum time warp altitude, and from there I was able to divide each orbital period by the max time warp at that altitude to find the real-time orbital period.
In conclusion, yes, it's one of the harder bits of rocket science, but, like all bits of rocket science, there are equations for it, and Wolfram Alpha knows all of the equations.
*Equatorial Radius and Mass can both be obtained from the sidebar on the KSP Wiki.
Get out and push!
Yes, I am serious. It works.
Go on an EVA, activate the jetpack, and fly against the prograde-facing side of the capsule. When you are nearly out of EVA fuel (right-click on the astronaut to check how much you have left), get back into the capsule and leave it again to refill. You can do this as often as you want.
It doesn't do much, but each time you bump against the capsule, you bump it back a bit reducing its velocity. With enough patience you can get the capsules trajectory sub-orbital. You only need to get the periapsis below 70km. Atmosphere friction will then do the rest and deorbit your craft. Then you just have to activate your parachute and recover the craft.
...you do have a parachute on the craft, don't you?
No? Well, then all you can do is:
Do a rescue mission.
In order to rescue a kerbonaut you will need to perform an orbital rendezvous. This is an advanced maneuver to pull off, and it is even more difficult when you haven't unlocked maneuver nodes yet. But learning it is very important because it is the prerequisite for docking which opens countless new opportunities.
Build a more powerful ship than the one you built before, especially with much more fuel on the upper stage. Then add a probe core, some batteries and solar panels so it can fly unmanned. When you play career and don't have the technology yet, you can also just stack two command pods on top of each other. It looks quite ugly, but it works. Before you launch the vehicle, go to the crew-tab in the vehicle building and make sure the pod for Jebediah is empty.
Launch the rescue vehicle a few minutes before Jeb passes over the KSP to make sure you get close to it.
During and after the launch try to get on an orbit which is almost the same as the one of the ship you want to meet. When you timed the launch right you will end up quite close to the target, but it is quite unlikely that you will get it perfectly right, especially on the first try. Likely you will end up a few degree in front or behind the target.
When the target is in front of you, go on a lower orbit. When it is behind you, go on a higher orbit. The vessel on the lower orbit will catch up to the one on the higher orbit. When you are within 5km of the target, you can boost directly into the direction to close the distance. When the ships are below 100m apart and have no relative speed towards each other, you can use an EVA to transfer Jeb to the rescue ship.
Best Answer
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.