Indeed, the pot heigh and diameter match perfectly. That's the "handle settings" I don't understand...
Olivier, the script that Zen Stoves generates is for a 'generic pot', which is based on an MSR Titan, but has handle cutouts that are not as deep as are needed. This was to try to make it clear how the script worked.
To get it to suit your MSR Titan, you need to adjust the values. Here are the values I've used for the Titan kettle:
/panHeight 86 def % height of pan
/panCircumf 364.4 def % circumference of pan outer walls immediately under rim
/handleWidthTop 30 def % width at top of pan handles
/handleWidthMid 8 def % width at shoulder of pan handles
/handleDepthMid 18 def % measured from top of pan to below top of handle
/handleWidthBot 6 def % width at bottom of pan handles
/handleDepth 72 def % measured from top of pan to lowest point on handle
The middle and bottom widths can usually be smaller than the top, because the handles are held together when you hold the pot in your hand. The sloping sides of the cone mean that the opening for the bottom of the handles is along the tapered handles, so the opening does not need to be as big.
Or, you could do as Red Fish suggests, and experiment with a paper template, starting with a small handle opening, and cutting small adjustments until the handle fits.
If you haven't downloaded the instructions file from ZenStoves, I would strongly advise it.