Hiya,
I'm glad to see your well after it. Firstly, don't trust what most meters will tell you about the output. This is twofold:
1 - most meters are not intended to read such high frequency AC voltage. So, they read low.
2 - Many meters have capacitance across the input that will load down the circuit.
Not to worry though. No harm, no foul. These inverters are tough.
Chances are, you're closer to your 3kV goal than you think. The reason lies in the behavior of the CCFL lamp. when cold, the lamp typically takes about 3x it's operating voltage in order to ionize the gas within.
The inverter is designed to provide this voltage, but must then reduce the voltage, or excessive current will flow. It does this by placing a small value capacitor in series between the lamp and inverter. this will generally be a sky-blue colored capacitor near the lamp's terminal.
This capacitor will limit your output, but I'd leave it in at first, because it will help protect your parts. Later, I might double or triple the value.
In any case, with no load you'll have much more than 900 V peak at the output :-)
You may want to simply purchase a voltage multiplier. I found a number on ebay, including this one:
http://www.ebay.com/itm/M3KV6-positive-high-voltage-DC-power-supply-multiplier-/270891537695?pt=LH_DefaultDomain_0&hash=item3f1264d51f
If you wish to build it from scratch, a Rectron R5000F-B will likely be a good rectifier. With that, a 2.2nF HV capacitor, such as a Murata DECE33J222ZC4B.
HV can be creepy when you don't have a way to discharge it, so you probably want a large value (ie 22meg), high voltage (4kV), resistor to place across the output of the multiplier.
If you choose to go Frankenstein with the output, you may want to place the whole thing in oil or pot it. I've found that I can trick silicon caulking into making a nice conformal layer by dissolving it in a heaver solvent, such as MEK. Then dip the part, allow it to dry, and set it aside a night for the silicon to harden. Don't rush the process with heat!
Best of Luck!
Mike