The best way to heat jars evenly I have found--and a heating pad will NOT give even heating--is covered in this thread. Forget about the holes. Your trouble could be a number of things. I'll cover some from order of most to least likely.1) Your not incubating around 85°F (lower 80s are good).
2) Your spore sryinge has an unusually high bacterial count which the mycelium is struggling with.
3) Your substrate is too wet or the water's pH is wacked. Use mineral water and make sure the substrate is moist but not soaking wet. If unsure, squeeze it really well before packing to squeeze out the extra water.
Aside from that, gas exchange is really of minimal importance for half pint colonization. It can speed it up a couple days, but there is something much more seriously wrong if it's taking you a month to colonize a jar.
ShroomGod