I think GS can handle this . Maybe Tony has done it already ?  
Maybe it will take a lot of time before this gaps really appear ( they won't appear visually , but one has to look for the SMA of each object ) . Nice sim to let work at night .  
 
Edit : this sim may take a lot of time , if one considers the orbital period of Jupiter is 10 years and if it takes lets say 100 revolutions to get some resonace pattern one gets 1000 years of simulation at least .

And here's the inclination vs the SMA - you can really see the asteroid families here too. (the clump at 5.2 AU in both graphs are the Trojans in Jupiter's orbit). I'll discuss it more later on when I have the time.  
 

I've done some partial Kirkwood gap simulations.  I'll dig it up for you later.  But I'll briefly describe it now.  I computed the semi-major axis of one of the resonant zones.  Let's just say for example that it is 3 AU (I'll look up the exact answer later).  I placed 100 objects evenly spaced from 2.9 to 3.1 AU, every 0.1 AU.  I ran it for a few million years.  When I was finished, all the objects between 2.99 and 3.01 were ejected, and the others were virtually undisturbed.  This confirmed that Jupiter will clear the gap at that resonance.
 
You can probably plot all the points you want in IDL.  Additionally, I've made my own graph creator in Visual Basic.  It doesn't have many features, but if you can give me the semi-major axes in text format, I can plot all of them for you.  One issue that might be a problem, is that the graph might be too crowded with over 100,000 points.  Even the gaps might appear full because of screen resolution.

First, a disclaimer:  The Kirkwood Gaps are not visible gaps like the Cassini Division in Saturn's rings.  There are pleanty of asteroids in the Kirkwood Gaps.  However, most of them are asteroids with semi-major axes that do not equal the gap distance, but with enough eccentricity that they can cross the gaps.  There are very few of them that possess semi-major axes equal to those of certain resonances.  So the Kirkwood Gaps are only gaps in a histogram of semi-major axes like the image Mal posted.
 
Here's the simulations I promised you:
 
Asteroids in Jupiter's 3:1 interior resonance go around the sun three times for every time one time Jupiter goes around the sun.  So their periods should be 1/3 Jupiter's period.  Jupiter's orbital period  is 4331.572 days.  So their orbital periods should be 4331.572 /3 = 1443.85733333333 days.  Using the formula , and converting everything into proper units (just use the calculator here: http://orbitsimulator.com/gravity/articles/formula55.html , enter  1443.85733333333 for P, choose "d" for units, enter 1 for mass and choose "solar masses" for unit, and choose AU for output units), asteroids in Jupiter's 3:1 interior resonance should have semi-major axes of 2.50 AU.
 
The simulation http://orbitsimulator.com/gravity/simulations/j3_1.gsim begins with an accurate representation of the solar system's 8 planets, plus Earth's moon and Pluto.  Then 90 massless objects are added near Jupiter's 3:1 interior resonance.  There are 10 each at:
 
2.46 AU
2.47 AU
2.48 AU
2.49 AU
2.50 AU
2.51 AU
2.52 AU
2.53 AU
2.54 AU
 
The objects are color-coded and are given names that reflect their initial semi-major axis.  For example, "2p47 28" has an initial semi-major axis of 2.47, and it is the 28th asteroid in the simulation.
 
Let the simulation run at a time step of 16384 seconds, and in 3 million years, you'll find that most of the objects that started at semi-major axes of 2.50 and 2.51 (2p50 nn & 2p51 nn) are no longer in circular orbits, and many have very high inclinations.  All other asteroids are virtually unchanged.
 
If you don't want to wait the simulated 3 million years, the simulation http://orbitsimulator.com/gravity/simulations/j3_1_3millionYears.gsim shows this system 3 million years later.  This simulation begins in "ecliptic view" so you can see the high inclinations.  Drag the scroll bar to the top to return to a top-down view.
 
 
 
 

The following animation is the result of a gsim simulation .  
600 bodies were created at 3AU+/- 40% , so simulating an asteroid belt ( 0 incl , 0 eccentricity) .  
The a and e of each body were saved in an output file , every 10 years .  
The sim was run for 8500 years at 16000 seconds.  
I wrote a small programm able to read the Gsim-output file and able to represent the a and e value of ech body . ( a is represented from left to right , e is represented bottom up ) .  
So each dot represnts a body .  
Pasting each screenshot ( every 100 years ) gives the following animation ....
One can see the bodies originally at e=0 .  
The eccentricity of each body increases with time .  
The 4 little dots at the left are Mercury ,...Mars . The stationary dot at the right represents Jupiter .  
One can see also some gaps are created ( fi 2 cm to the right of Mars ) . .
The screenshot which doesn't erase every previous picture shows the gaps more clearly than this animation . I'll try to post it also .

Cool, those are really interesting sims and graphs. (I'd play more with this myself but I don't have the time right now... but thanks for trying these things out!). It's interesting how you can watch the eccentricities increase over time in the animation that frankuitaalst did. What might be interesting is to see if including Saturn in the system makes any difference - I think there are some secular resonances (the nu 6 one?) that can affect the inclination - these are mentioned on page 315 of Solar System Dynamics.  
 
I got the asteroid data from astorb.dat , which can be found here: ftp://ftp.lowell.edu/pub/elgb/astorb.html
 
I stripped out the asteroid number, semimajor axis, eccentricity and inclination and used those to make the graphs. Note that the data contains asteroids outside the main belt, so if you're showing them on a graph and want to focus on the belt you have to trim the range of the graph axes. I'll attach the data in the next posts.

Here's the #, SMA, Ecc, and Inc for asteroids 100000-199999 in csv format