The jitter should be mainly overcome by setting correct phase, although depending on the crystal in your specific MD you may also have to adjust samplerate slightly. Also remember that games on MD may be either 256 or 320 pixels wide, so make sure you are on right profile for the game at hand.
Are you using 240p test suite to adjust phase? The checkerboard pattern really helps on this matter. The test suite also lets you check your RGB levels with the colour ramps, so I would really recommend it.