The E12 series isn't quite evenly spaced from an exponential standpoint.
1.0 1.2 1.5 2.2 2.7 3.3 3.9 4.7 5.1 5.6 6.8 8.2
For example, 10/3.3 is much closer to 3 than to 3.3. It is admittedly curious that the 12-per-decade series offers two ways of getting a 3:1 ratio within 1.3% (one is 10/3.3; the other is 8.2/2.7) but the best 2:1 ratios it offers are off by 3% or more (5.6/2.7 is 3.7% off; 6.8/3.3 is 3.03% off). On the other hand, since the E12 series is typically used with 10%-tolerance parts, the sloppiness of the ratios doesn't really matter.
The E24 series (5% parts) offers values of 2.0 and 3.0; the E96 and E192 series offer 2.00, but the closest they offer to 3.0 is 3.01.
Your gap is too wide. Make it very, very very narrow. And rolled into a cylinder. Like a real capacitor.
Yes, +q could be less than -q, but only if the attraction/repulsion effects of electrons in the connecting wires were nearly as large as the attraction/repulsion down between the capacitor plates. (In that case the plates wouldn't be a near-perfect electrical shield for the fields produced by the wires.) But with real-world capacitors, this doesn't happen, and instead the field between the plate is totally enormous compared to the tiny fields produced by electrons in the wires. If +q only differs from -q by a millionth of a percent, we ignore it. See Engineer's capacitor vs. Physicist's capacitor, a split metal ball, versus two separate balls.
For capacitors used in circuitry, if we dump some charge on one capacitor terminal, exactly half of it will seemingly migrate to the other terminal. Weird. But "physicist-style capacitors" with small, wide-spaced plates are different, and an extra electron on the wire will make +q not equal to -q.
In detail: if the capacitance across the plates is 10,000pF, and the capacitance to Earth of each wire and plate is 0.01 pF, then the opposite plate's charges will ignore any small +q and/or -q on the connecting wires. The attraction/repulsion of electrons in the wires doesn't significantly alter the enormous +q and -q on the inner side of the capacitor plates.
Engineers use real-world components: wide capacitor plates with very narrow gaps; gaps the thickness of insulating film. But if you were a physicist, your capacitors might be metal spheres with large gaps between, or metal disks where the space between the plates was large when compared to their diameter. (Or you'd draw a capacitor symbol where the gap between plates was enormous and easy to see.) In this case the attraction/repulsion of electrons on the connecting wires would have an effect on the balance of +q -q between capacitor plates.
PS
Another weird concept: make a solid stack of thousands of disc capacitors: foil disk, dielectric disk, foil disk, etc. Use half-inch wide disks, and stack them up into a narrow foot-long rod. Now connect one end to 1,000 volts. The same kilovolt will appear on the other end! The rod is acting like a conductor. Yet its DC resistance is just about infinite. Series capacitors! Each little capacitor induces charge on the next and the next, all the way to the end.
Best Answer
As I understand it, you want to make a 1 kV polarized capacitor from two polarized 500 V capacitors:
The bleeder resistors are intended to keep the voltages on the capacitors roughly balanced. OK so far, but this seems rather extreme.
The resistors will draw ½ A with 1 kV in! That's 500 W of power, and each resistor will dissipate 250 W. This might work if you're trying to make a small toaster, but then you wouldn't need the capacitors at all.
Another way to look at this is to see when the result looks mostly capacitive and when mostly resistive. The -3 dB point of 1 kΩ and 10 mF is 16 mHz. If all your frequencies will be substantially above 16 mHz, then you're actually OK from that point of view.
I would look carefully at the worst case this circuit will be subjected to and see if the resistors can't be made much larger.
Dissipating 500 W just to avoid more expensive high voltage caps seems like a poor tradeoff. Look at 1 kV caps, and also pop up a couple levels and re-examine why you think you need this in the first place.