Looks to me like you have more than one problem here.
The idle screw needs to screw in enough to lift the slide, hard to say how much, depends on how you drilled an tapped the hole... File some more of the boss on the carb if you think the screws are not penetrating enough.
Since it is backfiring, my guess is you have an airleak, make sure the choke tube is in place (little black tube 1/4 x 2"), carb tops are on properly and the boot clamps are tight.
On my bike, the markers are in the centre of the window.
What are your mods? Filter, pipes, etc?